KLIFS - the structural kinase database

Structure information


PDB:	5XV7
PubMed:	29478907
Release date:	2018-03-14
Resolution:	2.32 Å

Kinase:	SRPK1
Family:	SRPK
Group:	CMGC
Species:	HUMAN

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

DFG conformation:	in
αC-helix conformation:	in
Salt bridge K^III.17 and E^αC.24:	Yes (2.9Å)


ASP rotation (xDFG.81) :	319°
PHE rotation (xDFG.82) :	3°
Activation loop position:	-3.3Å
αC-helix position:	18.1Å

G-rich loop angle:	60.2°
G-rich loop distance:	18.6Å
G-rich loop rotation:	30.4°

2D & 3D views

Binding pocket waters

The following waters were found in the defined clusters:

I4

H-bond ligand

H-bond protein

Binding pocket sequence

Uniprot	RKLGWGHFSTVWLVAMKVVTALDEIRLLKSVREMVVQLLDDCMVFEVLG-HHLLKWIIKLHTKCRIIHTDIKPENILLIADLGNA
Structure:	RKLGWGHFSTVWLVAMKVVTALDEIRLLKSVREMVVQLLDDVMVFEVLG_HHLLKWIIKLHTKCRIIHTDIKPENILLIADLGNA

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: EMH
Ligand Name: 9-ethyl-6,6-dimethyl-8-[4-(morpholin-4-yl)piperidin-1-yl]-11-oxo-6,11-dihydro-5H-benzo[b]carbazole-3-carbonitrile

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LABELS
KLIFS residue #
Amino Acid
None
COLORS
Interaction types
KLIFS (all res.)
KLIFS (interacting res.)
None
OTHER
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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 R
84

2 K
85

3 L
86

4 G
87

5 W
88

6 G
89

7 H
90

8 F
91

9 S
92

10 T
93

11 V
94

12 W
95

13 L
96

14 V
106

15 A
107

16 M
108

17 K
109

18 V
110

19 V
111

20 T
120

■

αC

b.l

IV

21 A
121

22 L
122

23 D
123

24 E
124

25 I
125

26 R
126

27 L
127

28 L
128

29 K
129

30 S
130

31 V
131

32 R
132

33 E
142

34 M
143

35 V
144

36 V
145

37 Q
146

38 L
147

39 L
148

40 D
149

■

IV

V

GK

hinge

linker

αD

αE

41 D
150

42 V
162

43 M
163

44 V
164

45 F
165

46 E
166

47 V
167

48 L
168

49 G
169

50 _
_

51 H
170

52 H
171

53 L
172

54 L
173

55 K
174

56 W
175

57 I
176

58 I
177

59 K
178

60 L
203

■♦

■

■▲

■

αE

VI

c.l

VII

VIII

x

61 H
204

62 T
205

63 K
206

64 C
207

65 R
208

66 I
209

67 I
210

68 H
211

69 T
212

70 D
213

71 I
214

72 K
215

73 P
216

74 E
217

75 N
218

76 I
219

77 L
220

78 L
221

79 I
495

80 A
496

■

DFG

a.l

81 D
497

82 L
498

83 G
499

84 N
500

85 A
501

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL1738797
Bioaffinities: 25 records for 14 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	ALK tyrosine kinase receptor	8.3	7.7	8.7	pIC50	8
Homo sapiens	CaM-kinase kinase beta	4.5	4.5	4.5	pKd	1
Homo sapiens	Casein kinase I gamma 2	6.3	6.3	6.3	pKd	1
Homo sapiens	Dual specificity protein kinase CLK2	5.6	5.6	5.6	pKd	1
Homo sapiens	Dual specificity protein kinase CLK3	5.9	5.9	5.9	pKd	1
Homo sapiens	Dual specificty protein kinase CLK1	4.5	4.5	4.5	pKd	1
Homo sapiens	Ephrin type-A receptor 1	6.7	6.7	6.7	pKd	1
Homo sapiens	Phosphorylase kinase gamma subunit 2	5.8	5.8	5.8	pKd	1
Homo sapiens	Proto-oncogene tyrosine-protein kinase ROS	5.6	5.6	5.7	pKi	2
Homo sapiens	Serine/threonine-protein kinase GAK	6.6	6.6	6.6	pKd	1
Homo sapiens	Serine/threonine-protein kinase SRPK1	6.7	6.7	6.7	pIC50	1
Homo sapiens	Tyrosine-protein kinase FER	5.4	5.4	5.4	pKd	1
Homo sapiens	Tyrosine-protein kinase receptor RET	7.4	7.4	8.3	pIC50	2
Homo sapiens	Tyrosine-protein kinase receptor RET	6.4	6.4	6.4	pKd	1
Homo sapiens	Vascular endothelial growth factor receptor 2	5.9	5.9	5.9	pIC50	2

5XV7 - chain A | SRSF protein kinase 1