KLIFS - the kinase structures database

Version: 3.2
Updated: 29-Oct-2025

Kinase structure
Kinase:	KDR
Family:	VEGFR
Group:	TK
Species:	HUMAN
IUPHAR/BPS ID:	1813
PDB:	3EFL
sc-PDB:
KIDFamMap:	Search
Release date:	2009-09-15
Chain:	A
Orthosteric ligand:	706

More entries for 3EFL
3EFL	Chain:	B

Structural information
DFG conformation:	out
αC-helix conformation:	in
G-rich loop angle (distance):	59.9° (18.5Å)
G-rich loop rotation:	48.9°
Quality Score:	6.4
Resolution:	2.2 Å
Missing Residues:	4
Missing Atoms:	0

Ligand binding mode
Pockets	Subpockets	Waters
front gate back	BP-I-B BP-II-out	Cluster I1 I7	Ligand No No	Protein Yes Yes

Pocket alignment
Uniprot sequence:	KPLGRGAFGQVIEVAVKMLALMSELKILIHIGLNVVNLLGAMVIVEFCKFGNLSTYLRSFLASRKCIHRDLAARNILLICDFGLA
Sequence structure:	KPLGRG__GQVIEVAVKMLALMSELKILIHIGLNVVNLLGAMVIVEFCKFGNLSTYLRSFLASRKCIHRDLAARNILLICDFG__

Ligand affinity
ChEMBL ID:	CHEMBL572881
Bioaffinities:	129 records for 42 kinases

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Citron Rho-interacting kinase	6.5	6.5	6.5	pKd	2
Homo sapiens	Ephrin type-A receptor 6	6.3	6.3	6.3	pKd	2
Homo sapiens	Epidermal growth factor receptor erbB1	5.6	5.2	7.8	pKd	16
Homo sapiens	Epithelial discoidin domain-containing receptor 1	6.6	6.6	6.6	pKd	2
Homo sapiens	Eukaryotic translation initiation factor 2-alpha kinase 4	5.4	5.4	5.4	pKd	2
Homo sapiens	Fibroblast growth factor receptor 1	5.2	5.2	5.2	pKd	2
Homo sapiens	Fibroblast growth factor receptor 4	5.2	5.2	5.2	pKd	2
Homo sapiens	Macrophage colony stimulating factor receptor	8.3	8.3	8.3	pKd	2
Homo sapiens	Mitogen-activated protein kinase kinase kinase 2	5.2	5.2	5.2	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 3	5.7	5.7	5.7	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 7	5.9	5.9	5.9	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 4	5.2	5.2	5.2	pKd	1
Homo sapiens	Mixed lineage kinase 7	8.1	8.1	8.1	pKd	2
Homo sapiens	Platelet-derived growth factor receptor alpha	8	8	8	pKd	2
Homo sapiens	Platelet-derived growth factor receptor beta	8	8	8	pKd	2
Homo sapiens	Serine/threonine-protein kinase 10	6	6	6	pKd	2
Homo sapiens	Serine/threonine-protein kinase 2	5.9	5.9	5.9	pKd	2
Homo sapiens	Serine/threonine-protein kinase 35	5.3	5.3	5.3	pKd	1
Homo sapiens	Serine/threonine-protein kinase Aurora-C	5.7	5.7	5.7	pKd	2
Homo sapiens	Serine/threonine-protein kinase B-raf	6.2	6.2	6.6	pKd	4
Homo sapiens	Serine/threonine-protein kinase RAF	6.1	6.1	6.1	pKd	2
Homo sapiens	Serine/threonine-protein kinase RIPK2	5	5	5	pKd	1
Homo sapiens	Serine/threonine-protein kinase TNNI3K	6.7	6.7	6.7	pKd	2
Homo sapiens	SPS1/STE20-related protein kinase YSK4	6.7	6.7	6.7	pKd	1
Homo sapiens	Stem cell growth factor receptor	7.9	6.4	8.9	pKd	15
Homo sapiens	Tyrosine-protein kinase ABL	5.4	5.1	6.2	pKd	9
Homo sapiens	Tyrosine-protein kinase ABL2	5.4	5.4	5.4	pKd	1
Homo sapiens	Tyrosine-protein kinase BLK	5.7	5.7	5.7	pKd	2
Homo sapiens	Tyrosine-protein kinase BRK	6	6	6	pKd	2
Homo sapiens	Tyrosine-protein kinase FGR	5.2	5.2	5.2	pKd	2
Homo sapiens	Tyrosine-protein kinase FRK	7	7	7	pKd	2
Homo sapiens	Tyrosine-protein kinase FYN	5.6	5.6	5.6	pKd	2
Homo sapiens	Tyrosine-protein kinase HCK	5.1	5.1	5.1	pKd	1
Homo sapiens	Tyrosine-protein kinase JAK1	5.3	5.3	5.3	pKd	2
Homo sapiens	Tyrosine-protein kinase LCK	6.4	6.4	6.4	pKd	2
Homo sapiens	Tyrosine-protein kinase Lyn	6.8	6.8	6.8	pKd	2
Homo sapiens	Tyrosine-protein kinase receptor FLT3	6	5	7.3	pKd	11
Homo sapiens	Tyrosine-protein kinase receptor RET	7.1	7.1	7.2	pIC50	2
Homo sapiens	Tyrosine-protein kinase receptor RET	7.7	7.7	7.9	pKd	4
Homo sapiens	Tyrosine-protein kinase YES	5.3	5.3	5.3	pKd	1
Homo sapiens	Vascular endothelial growth factor receptor 1	8.7	8.7	8.7	pIC50	2
Homo sapiens	Vascular endothelial growth factor receptor 1	7.9	7.9	7.9	pKd	2
Homo sapiens	Vascular endothelial growth factor receptor 2	8.5	8.5	8.5	pIC50	3
Homo sapiens	Vascular endothelial growth factor receptor 2	7.6	7.6	7.6	pKd	2
Homo sapiens	Vascular endothelial growth factor receptor 3	8.2	8.2	8.2	pIC50	1
Homo sapiens	Vascular endothelial growth factor receptor 3	8	8	8	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 K
838

2 P
839

3 L
840

4 G
841

5 R
842

6 G
843

7 _
_

8 _
_

9 G
846

10 Q
847

11 V
848

12 I
849

13 E
850

14 V
865

15 A
866

16 V
867

17 K
868

18 M
869

19 L
870

20 A
881

•

αC

b.l

21 L
882

22 M
883

23 S
884

24 E
885

25 L
886

26 K
887

27 I
888

28 L
889

29 I
890

30 H
891

31 I
892

32 G
893

33 L
896

34 N
897

35 V
898

36 V
899

37 N
900

38 L
901

39 L
902

40 G
903

••

•

hinge

linker

αD

αE

41 A
904

42 M
913

43 V
914

44 I
915

45 V
916

46 E
917

47 F
918

48 C
919

49 K
920

50 F
921

51 G
922

52 N
923

53 L
924

54 S
925

55 T
926

56 Y
927

57 L
928

58 R
929

59 S
930

60 F
1018

•

••

αE

c.l

VII

VIII

61 L
1019

62 A
1020

63 S
1021

64 R
1022

65 K
1023

66 C
1024

67 I
1025

68 H
1026

69 R
1027

70 D
1028

71 L
1029

72 A
1030

73 A
1031

74 R
1032

75 N
1033

76 I
1034

77 L
1035

78 L
1036

79 I
1044

80 C
1045

•

DFG

a.l

81 D
1046

82 F
1047

83 G
1048

84 _
_

85 _
_

••

Interaction pattern search

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