KLIFS - the structural kinase database

Structure information


PDB:	1R0P
PubMed:	14559966
Release date:	2003-10-07
Resolution:	1.8 Å

Kinase:	MET
Family:	Met
Group:	TK
Species:	HUMAN

Quality Score:	8
Missing Residues:	0
Missing Atoms:	0

DFG conformation:	in
αC-helix conformation:	out
Salt bridge K^III.17 and E^αC.24:	No (8.5Å)


ASP rotation (xDFG.81) :	339°
PHE rotation (xDFG.82) :	356°
Activation loop position:	-3.2Å
αC-helix position:	21Å

G-rich loop angle:	66.3°
G-rich loop distance:	20Å
G-rich loop rotation:	48.2°

2D & 3D views

Binding pocket waters

No waters were found in the defined clusters

Binding pocket sequence

Uniprot	EVIGRGHFGCVYHCAVKSLQFLTEGIIMKDFSPNVLSLLGILVVLPYMKHGDLRNFIRNYLASKKFVHRDLAARNCMLVADFGLA
Structure:	EVIGRGHFGCVYHCAVKSLQFLTEGIIMKDFSPNVLSLLGILVVLPYMKHGDLRNFIRNFLASKKFVHRDLAARNCMLVADFGLA

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: KSA
Ligand Name: K-252A

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LABELS
KLIFS residue #
Amino Acid
None
COLORS
Interaction types
KLIFS (all res.)
KLIFS (interacting res.)
None
OTHER
Show/hide non-interacting res.
En/disable resizing interacting res.

This ligand targets the following (sub)pockets:

Main pockets
Front
Gate
Back

Subpockets
FP-I
FP-II
BP-I-A
BP-I-B
BP-II-in
BP-II-A-in
BP-II-B-in
BP-II-out
BP-II-B
BP-III
BP-IV
BP-V

Kinase-ligand interactions

■ Hydrophobic ♦ Aromatic face-to-face ♦ Aromatic face-to-edge ▲ H-bond donor ▲ H-bond acceptor ● Ionic positive ● Ionic negative

I

g.l

II

III

αC

1 E
1082

2 V
1083

3 I
1084

4 G
1085

5 R
1086

6 G
1087

7 H
1088

8 F
1089

9 G
1090

10 C
1091

11 V
1092

12 Y
1093

13 H
1094

14 C
1107

15 A
1108

16 V
1109

17 K
1110

18 S
1111

19 L
1112

20 Q
1123

■

αC

b.l

IV

21 F
1124

22 L
1125

23 T
1126

24 E
1127

25 G
1128

26 I
1129

27 I
1130

28 M
1131

29 K
1132

30 D
1133

31 F
1134

32 S
1135

33 P
1137

34 N
1138

35 V
1139

36 L
1140

37 S
1141

38 L
1142

39 L
1143

40 G
1144

IV

V

GK

hinge

linker

αD

αE

41 I
1145

42 L
1154

43 V
1155

44 V
1156

45 L
1157

46 P
1158

47 Y
1159

48 M
1160

49 K
1161

50 H
1162

51 G
1163

52 D
1164

53 L
1165

54 R
1166

55 N
1167

56 F
1168

57 I
1169

58 R
1170

59 N
1171

60 F
1194

■

▲

■♦

■▲

■

αE

VI

c.l

VII

VIII

x

61 L
1195

62 A
1196

63 S
1197

64 K
1198

65 K
1199

66 F
1200

67 V
1201

68 H
1202

69 R
1203

70 D
1204

71 L
1205

72 A
1206

73 A
1207

74 R
1208

75 N
1209

76 C
1210

77 M
1211

78 L
1212

79 V
1220

80 A
1221

■

DFG

a.l

81 D
1222

82 F
1223

83 G
1224

84 L
1225

85 A
1226

■

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL281948
Bioaffinities: 102 records for 92 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Activin receptor type-1B	4.8	4.8	4.8	pKd	1
Homo sapiens	Adaptor-associated kinase	8.3	8.3	8.3	pKd	1
Homo sapiens	AMP-activated protein kinase, alpha-1 subunit	6.3	6.3	6.3	pKd	1
Homo sapiens	BMP-2-inducible protein kinase	7.1	7.1	7.1	pKd	1
Homo sapiens	CaM kinase II delta	6.7	6.7	6.7	pKd	1
Homo sapiens	CaM kinase II gamma	6.8	6.8	6.8	pKd	1
Homo sapiens	CaM-kinase kinase beta	5.6	5.6	5.6	pKd	1
Homo sapiens	c-Jun N-terminal kinase 1	6.3	6.3	6.3	pKd	1
Homo sapiens	c-Jun N-terminal kinase 2	6	6	6	pKd	1
Homo sapiens	Cyclin-dependent kinase 2	7	7	7	pKd	1
Homo sapiens	Cyclin-dependent kinase 3	7.5	7.5	7.5	pKd	1
Homo sapiens	Cyclin-dependent kinase 4	7.9	7.9	7.9	pKd	1
Homo sapiens	Cyclin-dependent kinase 5	6	6	6	pKd	1
Homo sapiens	Cyclin-dependent kinase 6	6.4	6.4	6.4	pKd	1
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 1	5.8	5.8	5.8	pKd	1
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 2	6.3	6.3	6.3	pKd	1
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 5	5.7	5.7	5.7	pKd	1
Homo sapiens	Dual specificity mitogen-activated protein kinase kinase 6	7.1	7.1	7.1	pKd	1
Homo sapiens	Dual specificity protein kinase CLK2	5.4	5.4	5.4	pKd	1
Homo sapiens	Dual specificity protein kinase CLK4	7.8	7.8	7.8	pKd	1
Homo sapiens	Dual specificity protein kinase TTK	7.5	7.5	7.5	pKd	1
Homo sapiens	Dual-specificity tyrosine-phosphorylation regulated kinase 1A	5.3	5.3	5.3	pKd	1
Homo sapiens	Dual specificty protein kinase CLK1	8	8	8	pKd	1
Homo sapiens	Inhibitor of nuclear factor kappa B kinase epsilon subunit	6.3	6.3	6.3	pKd	1
Homo sapiens	Interleukin-1 receptor-associated kinase 3	6.6	6.6	6.6	pKd	1
Homo sapiens	Interleukin-1 receptor-associated kinase 4	8.1	8.1	8.1	pKd	1
Homo sapiens	MAP/microtubule affinity-regulating kinase 2	6.2	6.2	6.2	pKd	1
Homo sapiens	MAP/microtubule affinity-regulating kinase 4	7.6	7.6	7.6	pKd	1
Homo sapiens	Maternal embryonic leucine zipper kinase	7.1	7.1	7.1	pKd	1
Homo sapiens	Mitogen-activated protein kinase 15	6.8	6.8	6.8	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 11	6.2	6.2	6.2	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 2	5.4	5.4	5.4	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 5	6.7	6.7	6.7	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase 6	6.5	6.5	6.5	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 1	6.3	6.3	6.3	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 2	6.9	6.9	6.9	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 3	5.6	5.6	5.6	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 4	7.7	7.7	7.7	pKd	1
Homo sapiens	Mitogen-activated protein kinase kinase kinase kinase 5	6.7	6.7	6.7	pKd	1
Homo sapiens	Myosin light chain kinase	7	7	7	pKd	1
Homo sapiens	Myosin light chain kinase, smooth muscle	7.7	7.7	7.7	pIC50	1
Homo sapiens	Myosin light chain kinase, smooth muscle	7.7	7.7	7.7	pKi	1
Homo sapiens	Nerve growth factor receptor Trk-A	7.9	7.9	8.6	pIC50	3
Homo sapiens	Nerve growth factor receptor Trk-A	5.8	5.8	5.8	pKd	1
Homo sapiens	Non-receptor tyrosine-protein kinase TNK1	6.5	6.5	6.5	pKd	1
Homo sapiens	Phosphorylase kinase gamma subunit 2	5.5	5.5	5.5	pKd	1
Homo sapiens	Platelet-derived growth factor receptor beta	6	6	6	pKd	1
Homo sapiens	Protein kinase C alpha	5.6	5.6	5.6	pKd	1
Homo sapiens	Protein kinase C nu	7.4	7.4	7.4	pKd	1
Homo sapiens	Protein kinase C theta	6.3	6.3	6.3	pIC50	1
Homo sapiens	Protein kinase N1	6.6	6.6	6.6	pKd	1
Homo sapiens	Protein kinase N2	6.4	6.4	6.4	pKd	1
Homo sapiens	Protein tyrosine kinase 2 beta	5.9	5.9	5.9	pKd	1
Homo sapiens	Proto-oncogene tyrosine-protein kinase MER	7.4	7.4	7.4	pKd	1
Homo sapiens	Ribosomal protein S6 kinase alpha 1	5.5	5.5	5.5	pKd	2
Homo sapiens	Ribosomal protein S6 kinase alpha 3	5.5	5.5	5.5	pKd	2
Homo sapiens	Ribosomal protein S6 kinase alpha 4	6.4	6.4	6.4	pKd	2
Homo sapiens	Ribosomal protein S6 kinase alpha 5	4.8	4.8	4.8	pKd	2
Homo sapiens	Ribosomal protein S6 kinase alpha 6	5.7	5.7	5.7	pKd	2
Homo sapiens	Serine/threonine-protein kinase 10	6.3	6.3	6.3	pKd	1
Homo sapiens	Serine/threonine-protein kinase 2	5.5	5.5	5.5	pKd	1
Homo sapiens	Serine/threonine-protein kinase 38-like	5.7	5.7	5.7	pKd	1
Homo sapiens	Serine/threonine-protein kinase Aurora-A	7.7	7.7	7.7	pKd	1
Homo sapiens	Serine/threonine-protein kinase Aurora-B	6.5	6.5	6.5	pKd	1
Homo sapiens	Serine/threonine-protein kinase Chk1	6.9	6.9	6.9	pKd	1
Homo sapiens	Serine/threonine-protein kinase c-TAK1	6.4	6.4	6.4	pKd	1
Homo sapiens	Serine/threonine-protein kinase D2	7.5	7.5	7.5	pKd	1
Homo sapiens	Serine/threonine-protein kinase/endoribonuclease IRE1	7.7	7.7	7.7	pKd	1
Homo sapiens	Serine/threonine-protein kinase/endoribonuclease IRE2	6	6	6	pKd	1
Homo sapiens	Serine/threonine-protein kinase GAK	5.9	5.9	5.9	pKd	1
Homo sapiens	Serine/threonine-protein kinase LATS1	7.2	7.2	7.2	pKd	1
Homo sapiens	Serine/threonine-protein kinase LMTK3	7.1	7.1	7.1	pIC50	1
Homo sapiens	Serine/threonine-protein kinase MST1	7.5	7.5	7.5	pKd	1
Homo sapiens	Serine/threonine-protein kinase MST2	7.4	7.4	7.4	pKd	1
Homo sapiens	Serine/threonine-protein kinase NEK7	8.5	8.5	8.5	pKd	1
Homo sapiens	Serine/threonine-protein kinase PAK 4	6.5	6.5	6.5	pKd	1
Homo sapiens	Serine/threonine-protein kinase PLK4	7.1	7.1	7.1	pKd	1
Homo sapiens	Serine/threonine-protein kinase RIPK2	6.3	6.3	6.3	pKd	1
Homo sapiens	Serine/threonine-protein kinase SIK2	7.2	7.2	7.2	pKd	1
Homo sapiens	Serine/threonine-protein kinase SIK3	5.4	5.4	5.4	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO1	4.7	4.7	4.7	pKd	1
Homo sapiens	Serine/threonine-protein kinase TBK1	5.9	5.9	5.9	pKd	1
Homo sapiens	Serine/threonine-protein kinase ULK3	7	7	7	pKd	1
Homo sapiens	TGF-beta receptor type I	5.7	5.7	5.7	pKd	1
Homo sapiens	TP53-regulating kinase	5.4	5.4	5.4	pKd	1
Homo sapiens	TRAF2- and NCK-interacting kinase	8	8	8	pKd	1
Homo sapiens	Tyrosine kinase non-receptor protein 2	5.8	5.8	5.8	pKd	1
Homo sapiens	Tyrosine-protein kinase BTK	5.8	5.8	5.8	pKd	1
Homo sapiens	Tyrosine-protein kinase FER	6.3	6.3	6.3	pKd	1
Homo sapiens	Tyrosine-protein kinase receptor FLT3	6.6	6.6	6.6	pKd	1
Homo sapiens	Tyrosine-protein kinase receptor RET	6.2	6.2	6.2	pKd	1
Homo sapiens	Tyrosine-protein kinase SYK	6.3	6.3	6.3	pKd	1
Homo sapiens	Uncharacterized aarF domain-containing protein kinase 1	5.2	5.2	5.2	pKd	1
Homo sapiens	Vascular endothelial growth factor receptor 2	7.4	7.4	7.4	pIC50	2

1R0P - chain A | MET proto-oncogene, receptor tyrosine kinase