KLIFS - the kinase structures database

Version: 3.2
Updated: 29-Oct-2025

Kinase structure
Kinase:	EPHB4 (EphB4)
Family:	Eph
Group:	TK
Species:	HUMAN
IUPHAR/BPS ID:	1833
PDB:	6FNM
sc-PDB:
KIDFamMap:	Search
Release date:	2018-08-08
PubMed:	29928781
Chain:	A
(Alternate) Model:	A
Orthosteric ligand:	1N1

More entries for 6FNM
6FNM	Alternative model:	B	Chain:	A

Structural information
DFG conformation:	in
αC-helix conformation:	in
G-rich loop angle (distance):	62.7° (19Å)
G-rich loop rotation:	84°
Quality Score:	8
Resolution:	1.16 Å
Missing Residues:	0
Missing Atoms:	0

Ligand binding mode
Pockets	Subpockets	Waters
front gate	BP-I-A BP-I-B	Cluster I1 I5 I9 I10	Ligand No No No No	Protein Yes Yes No Yes

Pocket alignment
Uniprot sequence:	EVIGAGEFGEVCRVAIKTLEFLSEASIMGQFEPNIIRLEGVMILTEFMENGALDSFLRLYLAEMSYVHRDLAARNILVVSDFGLS
Sequence structure:	EVIGAGEFGEVCRVAIKTLEFLSEASIMGQFEPNIIRLEGVMILTEFMENGALDSFLRLYLAEMSYVHRDLAARNILVVSDFGLS

Ligand affinity
ChEMBL ID:	CHEMBL1421
Bioaffinities:	404 records for 131 kinases

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Activin receptor type-1	6.2	6.2	6.2	pKd	2
Homo sapiens	Activin receptor type-1	7.1	7.1	7.1	pKi	1
Homo sapiens	Activin receptor type-1B	6.5	6.5	6.5	pKd	2
Homo sapiens	Activin receptor type-2A	6.7	6.7	6.7	pKd	2
Homo sapiens	Activin receptor type-2B	6.2	6.2	6.2	pKd	2
Homo sapiens	Bone morphogenetic protein receptor type-1A	5.2	5.2	5.2	pKd	1
Homo sapiens	Bone morphogenetic protein receptor type-1B	7.3	7.3	7.3	pKd	1
Plasmodium falciparum (isolate 3D7)	Calcium-dependent protein kinase 1	6.2	6.2	6.2	pKd	1
Homo sapiens	Casein kinase I epsilon	5.8	5.8	5.8	pKd	2
Homo sapiens	Chaperone activity of bc1 complex-like, mitochondrial	6.7	6.7	6.7	pKd	2
Homo sapiens	Discoidin domain-containing receptor 2	8.7	6.1	9.4	pIC50	5
Homo sapiens	Discoidin domain-containing receptor 2	8.5	7.8	8.5	pKd	4
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 1	6	6	6	pKd	2
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 1	6.2	6.2	6.2	pKi	1
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 2	5.9	5.9	5.9	pKd	2
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 2	5.8	5.8	5.8	pKi	1
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 5	8.5	8.5	8.5	pKd	1
Homo sapiens	Dual specificity testis-specific protein kinase 1	7.5	7.5	7.5	pKd	2
Homo sapiens	Dual-specificity tyrosine-phosphorylation regulated kinase 3	5.9	5.9	5.9	pKi	1
Homo sapiens	Ephrin type-A receptor 1	8.4	8.4	8.4	pKd	2
Homo sapiens	Ephrin type-A receptor 2	6.9	6.9	6.9	pIC50	1
Homo sapiens	Ephrin type-A receptor 2	9.1	9.1	9.1	pKd	2
Homo sapiens	Ephrin type-A receptor 2	8.4	8.4	8.4	pKi	1
Homo sapiens	Ephrin type-A receptor 3	10	10	10	pKd	2
Homo sapiens	Ephrin type-A receptor 4	8.9	8.9	8.9	pKd	2
Homo sapiens	Ephrin type-A receptor 5	9.6	9.6	9.6	pKd	2
Homo sapiens	Ephrin type-A receptor 6	5.7	5.7	5.7	pKd	1
Homo sapiens	Ephrin type-A receptor 8	9.6	9.6	9.6	pKd	2
Homo sapiens	Ephrin type-B receptor 1	9.4	9.4	9.4	pKd	2
Homo sapiens	Ephrin type-B receptor 2	8.4	8.4	8.4	pIC50	1
Homo sapiens	Ephrin type-B receptor 2	9.4	9.4	9.4	pKd	2
Homo sapiens	Ephrin type-B receptor 3	8.2	8.2	8.2	pKd	2
Homo sapiens	Ephrin type-B receptor 4	9.5	9.5	9.5	pKd	2
Homo sapiens	Epidermal growth factor receptor erbB1	6.8	5.5	7.7	pIC50	5
Homo sapiens	Epidermal growth factor receptor erbB1	6.9	5.6	7.1	pKd	22
Homo sapiens	Epithelial discoidin domain-containing receptor 1	8.3	8.3	9.3	pIC50	2
Homo sapiens	Epithelial discoidin domain-containing receptor 1	9.2	9.2	9.2	pKd	2
Homo sapiens	Eukaryotic translation initiation factor 2-alpha kinase 4	5.8	5.8	5.8	pKd	2
Homo sapiens	Fibroblast growth factor receptor 1	6.1	6.1	6.1	pIC50	1
Homo sapiens	Fibroblast growth factor receptor 1	5.4	5.4	5.4	pKd	2
Homo sapiens	Fibroblast growth factor receptor 1	5.7	5.7	5.7	pKi	1
Homo sapiens	Fibroblast growth factor receptor 2	5.9	5.9	5.9	pKd	2
Homo sapiens	Fibroblast growth factor receptor 3	5.4	5.4	5.4	pKd	1
Homo sapiens	Fibroblast growth factor receptor 3	5.9	5.9	5.9	pKi	1
Homo sapiens	Interleukin-1 receptor-associated kinase 4	5.3	5.3	5.3	pKi	1
Homo sapiens	LIM domain kinase 1	6.9	6.9	6.9	pIC50	1
Homo sapiens	LIM domain kinase 1	6.2	6.2	6.2	pKd	2
Homo sapiens	LIM domain kinase 1	6.6	6.6	6.6	pKi	1
Homo sapiens	LIM domain kinase 2	7.1	7.1	7.1	pKd	2
Homo sapiens	Macrophage colony stimulating factor receptor	8.1	8.1	8.3	pIC50	2
Homo sapiens	Macrophage colony stimulating factor receptor	9.2	9.2	9.2	pKd	2
Homo sapiens	MAP kinase p38 alpha	7.6	6.3	7.6	pKd	5
Homo sapiens	MAP kinase p38 alpha	7.5	7.5	7.5	pKi	1
Homo sapiens	MAP kinase p38 beta	6.4	6.4	6.4	pKd	2
Homo sapiens	Misshapen-like kinase 1	6.4	6.4	6.4	pKd	1
Homo sapiens	Misshapen-like kinase 1	6.1	6.1	6.1	pKi	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 10	5.6	5.6	5.6	pKi	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 13	5.3	5.3	5.3	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 2	6.9	6.9	6.9	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 3	6.6	6.6	6.6	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 4	6.5	6.5	6.5	pKd	2
Homo sapiens	Mitogen-activated protein kinase kinase kinase 7	5.4	5.4	5.4	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 1	6	6	6	pKd	2
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 2	5.9	5.9	5.9	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 3	6.2	6.2	6.2	pKd	2
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 4	5.5	5.5	5.5	pKd	2
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 5	7.4	7.4	7.4	pKd	2
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 5	7.8	7.8	7.8	pKi	1
Homo sapiens	Mixed lineage kinase 7	7.4	7.4	7.4	pKd	2
Homo sapiens	Mixed lineage kinase 7	7.3	7.3	7.3	pKi	1
Homo sapiens	myosin light chain kinase 2	5.5	5.5	5.5	pKd	1
Homo sapiens	Myotonin-protein kinase	5.9	5.9	5.9	pKd	2
Homo sapiens	Platelet-derived growth factor receptor alpha	7.2	7.2	8	pIC50	2
Homo sapiens	Platelet-derived growth factor receptor alpha	9.3	9.3	9.3	pKd	2
Homo sapiens	Platelet-derived growth factor receptor alpha	8	8	8	pKi	1
Homo sapiens	Platelet-derived growth factor receptor beta	7.6	7.6	7.6	pIC50	1
Homo sapiens	Platelet-derived growth factor receptor beta	9.2	9.2	9.2	pKd	2
Homo sapiens	Platelet-derived growth factor receptor beta	8.9	8.9	8.9	pKi	1
Homo sapiens	Protein kinase N2	5.3	5.3	5.3	pKi	1
Homo sapiens	Receptor protein-tyrosine kinase erbB-2	6.2	6.2	6.2	pIC50	2
Homo sapiens	Receptor protein-tyrosine kinase erbB-2	5.9	5.9	5.9	pKd	2
Homo sapiens	Receptor protein-tyrosine kinase erbB-2	6.8	6.8	6.8	pKi	1
Homo sapiens	Receptor protein-tyrosine kinase erbB-4	7.3	7.3	7.3	pKd	1
Homo sapiens	Receptor protein-tyrosine kinase erbB-4	7.4	7.4	7.4	pKi	1
Homo sapiens	Receptor tyrosine-protein kinase erbB-3	7.8	7.8	7.8	pKd	1
Homo sapiens	Serine/threonine-protein kinase 10	5.9	5.9	5.9	pKd	2
Homo sapiens	Serine/threonine-protein kinase 2	6.1	6.1	6.1	pKd	2
Homo sapiens	Serine/threonine-protein kinase 2	6.2	6.2	6.2	pKi	1
Homo sapiens	Serine/threonine-protein kinase 25	5.5	5.5	5.5	pKd	1
Homo sapiens	Serine/threonine-protein kinase 35	6.1	6.1	6.1	pKd	1
Homo sapiens	Serine/threonine-protein kinase 36	6.7	6.7	6.7	pKd	2
Homo sapiens	Serine/threonine-protein kinase Aurora-A	5.6	5.6	5.6	pIC50	1
Homo sapiens	Serine/threonine-protein kinase Aurora-A	5	5	5	pKd	1
Homo sapiens	Serine/threonine-protein kinase Aurora-B	5.2	5.2	5.2	pIC50	1
Homo sapiens	Serine/threonine-protein kinase Aurora-B	5.9	5.9	5.9	pKi	1
Homo sapiens	Serine/threonine-protein kinase B-raf	6.2	6.2	6.3	pKd	4
Homo sapiens	Serine/threonine-protein kinase GAK	8.6	8.6	8.6	pKd	3
Homo sapiens	Serine/threonine-protein kinase MRCK-A	5.7	5.7	5.7	pKd	2
Homo sapiens	Serine/threonine-protein kinase MRCK-A	5.2	5.2	5.2	pKi	1
Homo sapiens	Serine/threonine-protein kinase MRCK beta	5.7	5.7	5.7	pKd	2
Homo sapiens	Serine/threonine-protein kinase MRCK gamma	5.9	5.9	5.9	pKd	2
Homo sapiens	Serine/threonine-protein kinase MST1	5.4	5.4	5.4	pKd	1
Homo sapiens	Serine/threonine-protein kinase MST4	5.7	5.7	5.7	pKd	2
Homo sapiens	Serine/threonine-protein kinase mTOR	4.5	4.5	4.5	pIC50	1
Homo sapiens	Serine/threonine-protein kinase Nek11	6.3	6.3	6.3	pKd	1
Homo sapiens	Serine/threonine-protein kinase NEK2	5.2	5.2	5.2	pKd	1
Homo sapiens	Serine/threonine protein kinase NLK	6.6	6.6	6.6	pKd	2
Homo sapiens	Serine/threonine-protein kinase PLK4	5.7	5.7	5.7	pKi	1
Homo sapiens	Serine/threonine-protein kinase RAF	6.8	6.8	6.8	pIC50	1
Homo sapiens	Serine/threonine-protein kinase RAF	6.2	6.2	6.2	pKd	2
Homo sapiens	Serine/threonine-protein kinase receptor R3	6.3	6.3	6.3	pKd	2
Homo sapiens	Serine/threonine-protein kinase RIPK2	7	7	7	pIC50	1
Homo sapiens	Serine/threonine-protein kinase RIPK2	7.5	7.5	7.5	pKd	2
Homo sapiens	Serine/threonine-protein kinase SBK1	5.9	5.9	5.9	pKd	1
Homo sapiens	Serine/threonine-protein kinase SIK1	8.4	8.4	8.4	pKd	2
Homo sapiens	Serine/threonine-protein kinase SIK2	8.2	8.2	8.2	pKd	2
Homo sapiens	Serine/threonine-protein kinase SIK2	9.1	9.1	9.1	pKi	1
Homo sapiens	Serine/threonine-protein kinase SIK3	7.6	7.6	7.6	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO1	6	6	6	pKi	1
Homo sapiens	Serine/threonine-protein kinase TAO2	5.3	5.3	5.3	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO3	5.6	5.6	5.6	pKd	1
Homo sapiens	Serine/threonine-protein kinase TNNI3K	8	8	8	pKd	2
Homo sapiens	Serine/threonine-protein kinase ULK3	5.3	5.3	5.3	pKd	1
Homo sapiens	Serine/threonine-protein kinase WEE1	5.2	5.2	5.2	pKd	3
Homo sapiens	SPS1/STE20-related protein kinase YSK4	7.1	7.1	7.1	pKd	1
Homo sapiens	Stem cell growth factor receptor	8.3	6.9	8.8	pIC50	9
Homo sapiens	Stem cell growth factor receptor	9.1	8.6	9.2	pKd	13
Homo sapiens	TGF-beta receptor type I	6.6	6.6	6.6	pKd	2
Homo sapiens	TGF-beta receptor type II	5.5	5.5	5.5	pKd	2
Homo sapiens	TRAF2- and NCK-interacting kinase	5.7	5.7	5.7	pKd	2
Homo sapiens	Tyrosine- and threonine-specific cdc2-inhibitory kinase	6.7	6.7	8.2	pIC50	2
Homo sapiens	Tyrosine- and threonine-specific cdc2-inhibitory kinase	6.9	6.8	6.9	pKd	3
Homo sapiens	Tyrosine- and threonine-specific cdc2-inhibitory kinase	7.1	7.1	9.3	pKi	2
Homo sapiens	Tyrosine kinase non-receptor protein 2	8.3	8.2	8.3	pKd	3
Homo sapiens	Tyrosine kinase non-receptor protein 2	8.6	8.6	8.6	pKi	1
Homo sapiens	Tyrosine-protein kinase ABL	8.5	5.8	9.8	pIC50	14
Homo sapiens	Tyrosine-protein kinase ABL	10.2	6.1	10.8	pKd	22
Homo sapiens	Tyrosine-protein kinase ABL2	9.8	9.8	9.8	pKd	2
Homo sapiens	Tyrosine-protein kinase BLK	9.7	9.7	9.7	pKd	2
Mus musculus	Tyrosine-protein kinase BLK	8.1	8.1	8.1	pIC50	1
Homo sapiens	Tyrosine-protein kinase BMX	8.9	8.9	8.9	pKd	2
Homo sapiens	Tyrosine-protein kinase BRK	8.1	8.1	8.1	pIC50	1
Homo sapiens	Tyrosine-protein kinase BRK	8.1	8.1	8.1	pKd	2
Homo sapiens	Tyrosine-protein kinase BRK	8.3	8.3	8.3	pKi	1
Homo sapiens	Tyrosine-protein kinase BTK	8.3	8.3	8.9	pIC50	3
Homo sapiens	Tyrosine-protein kinase BTK	8.9	8.9	8.9	pKd	2
Homo sapiens	Tyrosine-protein kinase CSK	9	9	9	pKd	2
Homo sapiens	Tyrosine-protein kinase FES	5.7	5.7	5.7	pKi	1
Homo sapiens	Tyrosine-protein kinase FGR	9.3	9.3	9.3	pKd	2
Homo sapiens	Tyrosine-protein kinase FRK	9.5	9.5	9.5	pKd	2
Homo sapiens	Tyrosine-protein kinase FYN	9.7	9.7	9.7	pIC50	1
Homo sapiens	Tyrosine-protein kinase FYN	9.1	9.1	9.1	pKd	2
Homo sapiens	Tyrosine-protein kinase HCK	9.5	9.5	9.5	pKd	2
Homo sapiens	Tyrosine-protein kinase HCK	9.5	9.5	9.5	pKi	1
Homo sapiens	Tyrosine-protein kinase ITK/TSK	6.6	6.6	6.6	pIC50	1
Homo sapiens	Tyrosine-protein kinase JAK2	6	6	6	pKd	4
Homo sapiens	Tyrosine-protein kinase JAK2	5.9	5.9	5.9	pKi	2
Homo sapiens	Tyrosine-protein kinase JAK3	6.2	6.2	6.2	pKd	2
Homo sapiens	Tyrosine-protein kinase LCK	8.5	8.4	9.4	pIC50	4
Homo sapiens	Tyrosine-protein kinase LCK	9.7	9.7	9.7	pKd	2
Mus musculus	Tyrosine-protein kinase LCK	10.2	10.2	10.2	pKi	1
Homo sapiens	Tyrosine-protein kinase Lyn	9.2	9.2	9.2	pKd	2
Homo sapiens	Tyrosine-protein kinase receptor FLT3	5.2	5	5.5	pKd	7
Homo sapiens	Tyrosine-protein kinase receptor RET	5.7	5.7	6.4	pIC50	2
Homo sapiens	Tyrosine-protein kinase receptor RET	6.1	5.5	6.4	pKd	5
Homo sapiens	Tyrosine-protein kinase receptor UFO	5.7	5.7	5.7	pKi	1
Gallus gallus	Tyrosine-protein kinase SRC	6.3	6.3	9.4	pIC50	2
Gallus gallus	Tyrosine-protein kinase SRC	8	8	8	pKd	1
Homo sapiens	Tyrosine-protein kinase SRC	9.2	7.9	9.5	pIC50	9
Homo sapiens	Tyrosine-protein kinase SRC	9.7	8	9.7	pKd	4
Homo sapiens	Tyrosine-protein kinase Srms	7.9	7.9	7.9	pKd	2
Homo sapiens	Tyrosine-protein kinase Srms	9.2	9.2	9.2	pKi	1
Homo sapiens	Tyrosine-protein kinase SYK	5.5	5.5	5.5	pKd	2
Homo sapiens	Tyrosine-protein kinase SYK	6.7	6.7	6.7	pKi	1
Homo sapiens	Tyrosine-protein kinase TEC	6.5	6.5	6.5	pIC50	1
Homo sapiens	Tyrosine-protein kinase TEC	7.9	7.9	7.9	pKd	2
Homo sapiens	Tyrosine-protein kinase TXK	9.5	9.5	9.5	pIC50	1
Homo sapiens	Tyrosine-protein kinase TXK	8.7	8.7	8.7	pKd	2
Homo sapiens	Tyrosine-protein kinase TYK2	5.8	5.8	7	pKd	4
Homo sapiens	Tyrosine-protein kinase YES	9.3	9.3	9.3	pIC50	3
Homo sapiens	Tyrosine-protein kinase YES	9.5	9.5	9.5	pKd	2
Homo sapiens	Vascular endothelial growth factor receptor 1	5.3	5.3	5.3	pKd	2
Homo sapiens	Vascular endothelial growth factor receptor 2	5.6	5.6	5.6	pIC50	1
Homo sapiens	Vascular endothelial growth factor receptor 2	5.5	5.5	5.5	pKd	1
Homo sapiens	Vascular endothelial growth factor receptor 2	5.9	5.9	5.9	pKi	1
Homo sapiens	Wee1-like protein kinase 2	6.3	6.3	6.7	pKd	2

Kinase-ligand interaction pattern

• Hydrophobic • Aromatic face-to-face • Aromatic face-to-edge • H-bond donor • H-bond acceptor • Ionic positive • Ionic negative

g.l

III

αC

1 E
619

2 V
620

3 I
621

4 G
622

5 A
623

6 G
624

7 E
625

8 F
626

9 G
627

10 E
628

11 V
629

12 C
630

13 R
631

14 V
644

15 A
645

16 I
646

17 K
647

18 T
648

19 L
649

20 E
660

•

αC

b.l

21 F
661

22 L
662

23 S
663

24 E
664

25 A
665

26 S
666

27 I
667

28 M
668

29 G
669

30 Q
670

31 F
671

32 E
672

33 P
674

34 N
675

35 I
676

36 I
677

37 R
678

38 L
679

39 E
680

40 G
681

•

hinge

linker

αD

αE

41 V
682

42 M
690

43 I
691

44 L
692

45 T
693

46 E
694

47 F
695

48 M
696

49 E
697

50 N
698

51 G
699

52 A
700

53 L
701

54 D
702

55 S
703

56 F
704

57 L
705

58 R
706

59 L
707

60 Y
730

•

••

•

•••

•

αE

c.l

VII

VIII

61 L
731

62 A
732

63 E
733

64 M
734

65 S
735

66 Y
736

67 V
737

68 H
738

69 R
739

70 D
740

71 L
741

72 A
742

73 A
743

74 R
744

75 N
745

76 I
746

77 L
747

78 V
748

79 V
756

80 S
757

•

DFG

a.l

81 D
758

82 F
759

83 G
760

84 L
761

85 S
762

Interaction pattern search

Search KLIFS for kinase-ligand complexes with similar interaction patterns: