KLIFS - the kinase structures database

Version: 3.2
Updated: 05-Nov-2025

Neurotrophic tyrosine kinase, receptor, type 2

Kinase structure
Kinase:	NTRK2 (TRKB)
Family:	Trk
Group:	TK
Species:	HUMAN
IUPHAR/BPS ID:	1818
PDB:	4AT4
sc-PDB:
KIDFamMap:	Search
Release date:	2012-08-22
PubMed:	22902478
Chain:	A
Orthosteric ligand:	T6E

Structural information
DFG conformation:	out
αC-helix conformation:	out
G-rich loop angle (distance):	67° (19.9Å)
G-rich loop rotation:	63.3°
Quality Score:	6.8
Resolution:	2.36 Å
Missing Residues:	0
Missing Atoms:	0

Ligand binding mode
Pockets	Subpockets	Waters
front gate back	BP-I-B BP-II-out BP-III	Cluster I1	Ligand No	Protein Yes

Pocket alignment
Uniprot sequence:	RELGEGAFGKVFLVAVKTLDFHREAELLTNLQEHIVKFYGVIMVFEYMKHGDLNKFLRAYLASQHFVHRDLATRNCLVIGDFGMS
Sequence structure:	RELGEGAFGKVFLVAVKTLDFHREAELLTNLQEHIVKFYGVIMVFEYMKHGDLNKFLRAYLASQHFVHRDLATRNCLVIGDFGMS

Ligand affinity
ChEMBL ID:	CHEMBL1998585
Bioaffinities:	92 records for 88 kinases

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	3-phosphoinositide dependent protein kinase-1	6.1	6.1	6.1	pKi	1
Homo sapiens	ALK tyrosine kinase receptor	7.9	7.9	7.9	pKi	1
Homo sapiens	BR serine/threonine-protein kinase 1	6	6	6	pKi	1
Homo sapiens	CaM kinase I alpha	5.6	5.6	5.6	pKi	1
Homo sapiens	CaM kinase II beta	5.5	5.5	5.5	pKi	1
Homo sapiens	CaM kinase II delta	5.5	5.5	5.5	pKi	1
Homo sapiens	CaM kinase II gamma	5.9	5.9	5.9	pKi	1
Homo sapiens	Casein kinase I alpha	5.3	5.3	5.3	pKi	1
Homo sapiens	Casein kinase I delta	5.6	5.6	5.6	pKi	1
Homo sapiens	Casein kinase I gamma 1	5.5	5.5	5.5	pKi	1
Homo sapiens	Casein kinase I gamma 2	5.3	5.3	5.3	pKi	1
Homo sapiens	c-Jun N-terminal kinase 2	6.9	6.9	6.9	pKi	1
Homo sapiens	Cyclin-dependent kinase 1	5.2	5.2	5.2	pKi	1
Homo sapiens	Death-associated protein kinase 3	6.9	6.9	6.9	pKi	1
Homo sapiens	Dual specificity protein kinase CLK2	5.4	5.4	5.4	pKi	1
Homo sapiens	Dual specificity protein kinase CLK4	5.9	5.9	5.9	pKi	1
Homo sapiens	Dual-specificity tyrosine-phosphorylation regulated kinase 1A	5.2	5.2	5.2	pKi	1
Homo sapiens	Dual-specificity tyrosine-phosphorylation regulated kinase 3	5.6	5.6	5.6	pKi	1
Homo sapiens	Ephrin type-A receptor 2	7.4	7.4	7.4	pKi	1
Homo sapiens	Fibroblast growth factor receptor 1	7.7	7.7	7.7	pKi	1
Homo sapiens	Fibroblast growth factor receptor 3	7.2	7.2	7.2	pKi	1
Homo sapiens	Focal adhesion kinase 1	7.1	7.1	7.1	pKi	1
Homo sapiens	Glycogen synthase kinase-3 alpha	5.2	5.2	5.2	pKi	1
Homo sapiens	Glycogen synthase kinase-3 beta	6	6	6	pKi	1
Homo sapiens	Hepatocyte growth factor receptor	6.2	6.2	6.2	pKi	1
Homo sapiens	Homeodomain-interacting protein kinase 2	6.4	6.4	6.4	pKi	1
Homo sapiens	Homeodomain-interacting protein kinase 4	7.9	7.9	7.9	pKi	1
Homo sapiens	Insulin receptor	5.8	5.8	5.8	pKi	1
Homo sapiens	Interleukin-1 receptor-associated kinase 1	5.9	5.9	5.9	pKi	1
Homo sapiens	LIM domain kinase 1	5.4	5.4	5.4	pKi	1
Homo sapiens	Macrophage colony stimulating factor receptor	7.7	7.7	7.7	pKi	1
Homo sapiens	MAP kinase p38 delta	6.9	6.9	6.9	pKi	1
Homo sapiens	MAP kinase p38 gamma	6.4	6.4	6.4	pKi	1
Homo sapiens	MAP kinase signal-integrating kinase 2	6.4	6.4	6.4	pKi	1
Homo sapiens	MAP/microtubule affinity-regulating kinase 2	6.4	6.4	6.4	pKi	1
Homo sapiens	Maternal embryonic leucine zipper kinase	6.6	6.6	6.6	pKi	1
Homo sapiens	Misshapen-like kinase 1	6.4	6.4	6.4	pKi	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 2	6.6	6.6	6.6	pKi	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 4	6.1	6.1	6.1	pKi	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 5	7.6	7.6	7.6	pKi	1
Homo sapiens	Mixed lineage kinase 7	5.8	5.8	5.8	pKi	1
Homo sapiens	Nerve growth factor receptor Trk-A	8	8	8	pKi	1
Homo sapiens	Neurotrophic tyrosine kinase receptor type 2	7.9	7.9	7.9	pKi	1
Homo sapiens	NT-3 growth factor receptor	8.6	8.6	8.6	pKi	1
Homo sapiens	Protein kinase C nu	5.4	5.4	5.4	pKi	1
Homo sapiens	Protein tyrosine kinase 2 beta	6.9	6.9	6.9	pKi	1
Homo sapiens	Proto-oncogene tyrosine-protein kinase ROS	6.4	6.4	6.4	pKi	1
Homo sapiens	Rho-associated protein kinase 1	6.7	6.7	6.7	pKi	1
Homo sapiens	Rho-associated protein kinase 2	6.3	6.3	6.3	pKi	1
Homo sapiens	Ribosomal protein S6 kinase 1	7.6	7.6	7.6	pKi	1
Homo sapiens	Ribosomal protein S6 kinase alpha 3	6.6	6.6	6.6	pKi	2
Homo sapiens	Ribosomal protein S6 kinase alpha 4	7.1	7.1	7.1	pKi	2
Homo sapiens	Ribosomal protein S6 kinase alpha 5	6.2	6.2	6.2	pKi	2
Homo sapiens	Serine/threonine-protein kinase 2	7.7	7.7	7.7	pKi	1
Homo sapiens	Serine/threonine-protein kinase 33	5.6	5.6	5.6	pKi	1
Homo sapiens	Serine/threonine-protein kinase Aurora-A	6.7	6.7	6.7	pKi	1
Homo sapiens	Serine/threonine-protein kinase Chk2	5.5	5.5	5.5	pKi	1
Homo sapiens	Serine/threonine-protein kinase c-TAK1	7	7	7	pKi	1
Homo sapiens	Serine/threonine-protein kinase D2	5.2	5.2	5.2	pKi	1
Homo sapiens	Serine/threonine-protein kinase MST2	6.1	6.1	6.1	pKi	1
Homo sapiens	Serine/threonine-protein kinase NEK2	5.9	5.9	5.9	pKi	1
Homo sapiens	Serine/threonine-protein kinase Nek4	6.1	6.1	6.1	pKi	1
Homo sapiens	Serine/threonine-protein kinase PIM1	5.2	5.2	5.2	pKi	1
Homo sapiens	Serine/threonine-protein kinase PLK3	7.2	7.2	7.2	pKi	1
Homo sapiens	Serine/threonine-protein kinase PLK4	7.2	7.2	7.2	pKi	1
Homo sapiens	Serine/threonine-protein kinase Sgk2	5.5	5.5	5.5	pKi	1
Homo sapiens	Serine/threonine-protein kinase SRPK1	6	6	6	pKi	1
Homo sapiens	Serine/threonine-protein kinase TAO1	6.6	6.6	6.6	pKi	1
Homo sapiens	Stem cell growth factor receptor	7.4	7.4	7.4	pKi	1
Homo sapiens	Tyrosine-protein kinase ABL	7.5	7.5	7.5	pKi	1
Homo sapiens	Tyrosine-protein kinase BLK	7	7	7	pKi	1
Homo sapiens	Tyrosine-protein kinase BRK	6	6	6	pKi	1
Homo sapiens	Tyrosine-protein kinase BTK	6.2	6.2	6.2	pKi	1
Homo sapiens	Tyrosine-protein kinase CTK	6.8	6.8	6.8	pKi	1
Homo sapiens	Tyrosine-protein kinase FER	6.6	6.6	6.6	pKi	1
Homo sapiens	Tyrosine-protein kinase FES	6.1	6.1	6.1	pKi	1
Homo sapiens	Tyrosine-protein kinase FRK	8.3	8.3	8.3	pKi	1
Homo sapiens	Tyrosine-protein kinase FYN	7.1	7.1	7.1	pKi	1
Homo sapiens	Tyrosine-protein kinase ITK/TSK	6.4	6.4	6.4	pKi	1
Homo sapiens	Tyrosine-protein kinase JAK2	6.8	6.8	6.8	pKi	2
Homo sapiens	Tyrosine-protein kinase LCK	6.9	6.9	6.9	pKi	1
Homo sapiens	Tyrosine-protein kinase Lyn	7.2	7.2	7.2	pKi	1
Homo sapiens	Tyrosine-protein kinase receptor FLT3	8.7	8.7	8.7	pKi	1
Homo sapiens	Tyrosine-protein kinase receptor RET	8	8	8	pKi	1
Homo sapiens	Tyrosine-protein kinase receptor TYRO3	6.7	6.7	6.7	pKi	1
Homo sapiens	Tyrosine-protein kinase receptor UFO	8.9	8.9	8.9	pKi	1
Homo sapiens	Tyrosine-protein kinase SYK	6.6	6.6	6.6	pKi	1
Homo sapiens	Vascular endothelial growth factor receptor 1	8.6	8.6	8.6	pKi	1

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 R
558

2 E
559

3 L
560

4 G
561

5 E
562

6 G
563

7 A
564

8 F
565

9 G
566

10 K
567

11 V
568

12 F
569

13 L
570

14 V
585

15 A
586

16 V
587

17 K
588

18 T
589

19 L
590

20 D
600

•

αC

b.l

21 F
601

22 H
602

23 R
603

24 E
604

25 A
605

26 E
606

27 L
607

28 L
608

29 T
609

30 N
610

31 L
611

32 Q
612

33 E
614

34 H
615

35 I
616

36 V
617

37 K
618

38 F
619

39 Y
620

40 G
621

•

hinge

linker

αD

αE

41 V
622

42 I
630

43 M
631

44 V
632

45 F
633

46 E
634

47 Y
635

48 M
636

49 K
637

50 H
638

51 G
639

52 D
640

53 L
641

54 N
642

55 K
643

56 F
644

57 L
645

58 R
646

59 A
647

60 Y
682

••

•

••

αE

c.l

VII

VIII

61 L
683

62 A
684

63 S
685

64 Q
686

65 H
687

66 F
688

67 V
689

68 H
690

69 R
691

70 D
692

71 L
693

72 A
694

73 T
695

74 R
696

75 N
697

76 C
698

77 L
699

78 V
700

79 I
708

80 G
709

•

••

•

DFG

a.l

81 D
710

82 F
711

83 G
712

84 M
713

85 S
714

••

•

Interaction pattern search

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