KLIFS - the structural kinase database

Structure information


PDB:	2RKU
PubMed:	18005335
Release date:	2008-02-05
Resolution:	1.95 Å

Kinase:	PLK1
Family:	PLK
Group:	Other
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 (3.1Å)


ASP rotation (xDFG.81) :	350°
PHE rotation (xDFG.82) :	13°
Activation loop position:	-3.1Å
αC-helix position:	17.9Å

G-rich loop angle:	59°
G-rich loop distance:	16.4Å
G-rich loop rotation:	68.4°

Other models from this PDB:

2D & 3D views

Binding pocket waters

The following waters were found in the defined clusters:

I1

H-bond protein

I2

H-bond protein

I4

H-bond protein

I5

H-bond ligand

H-bond protein

I10

H-bond ligand

H-bond protein

Binding pocket sequence

Uniprot	RFLGKGGFAKCFEFAGKIVKMSMEISIHRSLAQHVVGFHGFFVVLELCRRRSLLELHKRYLHRNRVIHRDLKLGNLFLIGDFGLA
Structure:	RFLGKGGFAKCFEFAGKIVKMSMEISIHRSLAQHVVGFHGFFVVLELCRRRSLLELHKRYLHRNRVIHRDLKLGNLFLIGDFGLA

Modified residues

No modified residues identified.

Orthosteric ligand

Ligand HET-code: R78
Ligand Name: 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide

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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 R
57

2 F
58

3 L
59

4 G
60

5 K
61

6 G
62

7 G
63

8 F
64

9 A
65

10 K
66

11 C
67

12 F
68

13 E
69

14 F
79

15 A
80

16 G
81

17 K
82

18 I
83

19 V
84

20 K
97

■

■▲

■

αC

b.l

IV

21 M
98

22 S
99

23 M
100

24 E
101

25 I
102

26 S
103

27 I
104

28 H
105

29 R
106

30 S
107

31 L
108

32 A
109

33 Q
111

34 H
112

35 V
113

36 V
114

37 G
115

38 F
116

39 H
117

40 G
118

■

IV

V

GK

hinge

linker

αD

αE

41 F
119

42 F
127

43 V
128

44 V
129

45 L
130

46 E
131

47 L
132

48 C
133

49 R
134

50 R
135

51 R
136

52 S
137

53 L
138

54 L
139

55 E
140

56 L
141

57 H
142

58 K
143

59 R
144

60 Y
166

■

■▲▲

■

αE

VI

c.l

VII

VIII

x

61 L
167

62 H
168

63 R
169

64 N
170

65 R
171

66 V
172

67 I
173

68 H
174

69 R
175

70 D
176

71 L
177

72 K
178

73 L
179

74 G
180

75 N
181

76 L
182

77 F
183

78 L
184

79 I
192

80 G
193

■♦

DFG

a.l

81 D
194

82 F
195

83 G
196

84 L
197

85 A
198

Interaction pattern search

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

Binding affinities

ChEMBL ID:CHEMBL513909
Bioaffinities: 152 records for 83 kinase(s)

Species	Kinase (ChEMBL naming)	Median	Min	Max	Type	Records
Homo sapiens	Adaptor-associated kinase	5.6	5.6	5.6	pKd	1
Homo sapiens	ALK tyrosine kinase receptor	6.4	6.1	6.8	pIC50	3
Homo sapiens	ALK tyrosine kinase receptor	6.8	6.8	6.8	pKd	1
Homo sapiens	Bromodomain-containing protein 4	7.2	6.5	7.6	pIC50	11
Homo sapiens	Bromodomain-containing protein 4	7.4	7.1	7.6	pKd	5
Homo sapiens	Bromodomain-containing protein 4	7.3	7.3	7.3	pKi	1
Homo sapiens	Bromodomain testis-specific protein	5.9	5.9	6.6	pIC50	2
Homo sapiens	CaM kinase I delta	5.3	5.3	5.3	pKd	1
Homo sapiens	CaM kinase II alpha	5.9	5.9	5.9	pKd	1
Homo sapiens	CaM kinase II beta	5.4	5.4	5.4	pKd	1
Homo sapiens	CaM kinase II delta	5.6	5.6	5.6	pKd	1
Homo sapiens	CaM kinase II gamma	5.9	5.9	5.9	pKd	1
Homo sapiens	CaM-kinase kinase alpha	7.7	7.7	7.7	pKd	1
Homo sapiens	CaM-kinase kinase beta	6.6	6.6	7.6	pKd	2
Homo sapiens	Casein kinase I alpha	5.5	5.5	5.5	pKd	1
Homo sapiens	Casein kinase I delta	5.8	5.8	5.8	pKd	1
Homo sapiens	Casein kinase I epsilon	5.1	5.1	6.4	pKd	2
Homo sapiens	Casein kinase I gamma 1	5.4	5.4	5.4	pKd	1
Homo sapiens	Casein kinase I gamma 2	5.2	5.2	5.2	pKd	1
Homo sapiens	Casein kinase I isoform gamma-3	5.6	5.6	5.6	pKd	1
Homo sapiens	Citron Rho-interacting kinase	5.3	5.3	5.3	pKd	1
Homo sapiens	c-Jun N-terminal kinase 3	6	6	6	pKd	1
Homo sapiens	Cyclin-dependent kinase 4	5.7	5.7	5.7	pKd	1
Homo sapiens	Cyclin-dependent kinase 7	5.5	5.5	5.5	pKd	1
Homo sapiens	Death-associated protein kinase 1	6.3	6.3	6.3	pKd	1
Homo sapiens	Death-associated protein kinase 2	6	6	6	pKd	1
Homo sapiens	Death-associated protein kinase 3	6.9	6.9	6.9	pKd	1
Homo sapiens	Dual specificity protein kinase CLK2	6.3	6.3	6.3	pKd	1
Homo sapiens	Dual specificity protein kinase CLK3	6.2	6.2	6.2	pKd	1
Homo sapiens	Dual specificity protein kinase TTK	5.6	5.6	5.6	pKd	1
Homo sapiens	Dual specificty protein kinase CLK1	6	6	6	pKd	1
Homo sapiens	Epidermal growth factor receptor erbB1	5.7	5.2	6.6	pKd	12
Homo sapiens	Focal adhesion kinase 1	6.4	6.4	6.8	pKd	2
Homo sapiens	G protein-coupled receptor kinase 7	6.1	6.1	6.1	pKd	1
Homo sapiens	Hepatocyte growth factor receptor	5.6	5.6	5.6	pKd	1
Homo sapiens	Homeodomain-interacting protein kinase 1	5.4	5.4	5.4	pKd	1
Homo sapiens	Homeodomain-interacting protein kinase 2	5.5	5.5	5.5	pKd	1
Homo sapiens	Homeodomain-interacting protein kinase 3	5.4	5.4	5.4	pKd	1
Homo sapiens	Homeodomain-interacting protein kinase 4	5.7	5.7	5.7	pKd	1
Homo sapiens	Hormonally up-regulated neu tumor-associated kinase	5	5	5	pKd	1
Homo sapiens	Interferon-induced, double-stranded RNA-activated protein kinase	6.3	6.3	6.3	pKd	1
Homo sapiens	Interleukin-1 receptor-associated kinase 1	5.7	5.7	5.7	pKd	1
Homo sapiens	Interleukin-1 receptor-associated kinase 4	5.7	5.7	5.7	pKd	1
Homo sapiens	Leukocyte tyrosine kinase receptor	5.9	5.9	5.9	pKd	1
Homo sapiens	Misshapen-like kinase 1	5.8	5.8	5.8	pKd	1
Homo sapiens	Mitogen-activated protein kinase 7	5.5	5.5	5.5	pKd	1
Homo sapiens	Myosin IIIA	5.2	5.2	5.2	pKd	1
Homo sapiens	Myosin-IIIB	5.5	5.5	5.5	pKd	1
Homo sapiens	Myosin light chain kinase, smooth muscle	7	7	7	pKd	1
Homo sapiens	Myotonin-protein kinase	5.5	5.5	5.5	pKd	1
Homo sapiens	Phosphatidylinositol-5-phosphate 4-kinase type-2 gamma	5.6	5.6	7	pKd	2
Homo sapiens	Phosphorylase kinase gamma subunit 2	5.7	5.7	5.8	pKd	2
Homo sapiens	PI3-kinase p110-delta subunit	5.1	5.1	5.1	pKd	1
Homo sapiens	Protein kinase C mu	6.5	6.5	6.5	pKd	1
Homo sapiens	Protein kinase C nu	6.5	6.5	6.5	pKd	1
Homo sapiens	Protein tyrosine kinase 2 beta	6.5	6.5	6.5	pKd	1
Homo sapiens	Proto-oncogene tyrosine-protein kinase MER	5.5	5.5	5.5	pKd	1
Homo sapiens	Ribosomal protein S6 kinase alpha 1	5.3	5.3	5.3	pKd	2
Homo sapiens	Ribosomal protein S6 kinase alpha 2	6.2	6.2	6.2	pKd	2
Homo sapiens	Ribosomal protein S6 kinase alpha 4	7.9	7.9	7.9	pKd	2
Homo sapiens	Ribosomal protein S6 kinase alpha 5	6.6	6.6	6.6	pKd	2
Homo sapiens	Ribosomal protein S6 kinase alpha 6	5.9	5.9	5.9	pKd	2
Homo sapiens	Serine/threonine-protein kinase 10	5.3	5.3	5.3	pKd	1
Homo sapiens	Serine/threonine-protein kinase 16	6	6	6	pKd	1
Homo sapiens	Serine/threonine-protein kinase 2	5.4	5.4	5.4	pKd	1
Homo sapiens	Serine/threonine-protein kinase 33	6	6	6	pKd	1
Homo sapiens	Serine/threonine-protein kinase Chk2	5.1	5.1	5.1	pKd	1
Homo sapiens	Serine/threonine-protein kinase D2	5.7	5.7	6.3	pKd	2
Homo sapiens	Serine/threonine-protein kinase DCLK1	5.2	5.2	5.2	pKd	1
Homo sapiens	Serine/threonine-protein kinase GAK	5.3	5.3	6.8	pKd	2
Homo sapiens	Serine/threonine-protein kinase NEK2	5.7	5.7	5.7	pKd	1
Homo sapiens	Serine/threonine-protein kinase Nek3	6.1	6.1	6.1	pKd	1
Homo sapiens	Serine/threonine-protein kinase NEK7	5.2	5.2	5.2	pKd	1
Homo sapiens	Serine/threonine-protein kinase NIM1	6.1	6.1	6.1	pKd	1
Homo sapiens	Serine/threonine-protein kinase PLK1	9.1	6.1	9.1	pIC50	12
Homo sapiens	Serine/threonine-protein kinase PLK1	9.7	9.7	9.7	pKd	2
Homo sapiens	Serine/threonine-protein kinase PLK1	8.5	8.5	9.7	pKi	2
Homo sapiens	Serine/threonine-protein kinase PLK2	7.9	7.5	7.9	pIC50	3
Homo sapiens	Serine/threonine-protein kinase PLK2	9.1	9.1	9.1	pKd	1
Homo sapiens	Serine/threonine-protein kinase PLK3	7.7	7.1	7.7	pIC50	3
Homo sapiens	Serine/threonine-protein kinase PLK3	8.4	8.4	8.4	pKd	1
Homo sapiens	Serine/threonine-protein kinase RIO1	5.7	5.7	5.7	pKd	1
Homo sapiens	Serine/threonine-protein kinase RIO3	5.4	5.4	5.4	pKd	1
Homo sapiens	Serine/threonine-protein kinase TAO3	5.8	5.8	5.8	pKd	1
Homo sapiens	SPS1/STE20-related protein kinase YSK4	6.3	6.3	6.3	pKd	1
Homo sapiens	Transcription initiation factor TFIID subunit 1	6.8	6.8	6.8	pIC50	1
Homo sapiens	Transcription initiation factor TFIID subunit 1	6.8	6.8	6.8	pKd	1
Homo sapiens	Tyrosine-protein kinase ABL	5.6	5.2	5.7	pKd	5
Homo sapiens	Tyrosine-protein kinase FES	5.7	5.7	5.7	pKd	1
Homo sapiens	Tyrosine-protein kinase receptor FLT3	5.5	5.5	5.5	pKd	1
Homo sapiens	Tyrosine-protein kinase SYK	5.3	5.3	5.3	pKd	1

2RKU - chain A (model A) | Polo like kinase 1

Structure information

2D & 3D views

Binding pocket waters

Binding pocket sequence

Modified residues

Orthosteric ligand

Kinase-ligand interactions

Interaction pattern search

Binding affinities