4J52 - chain A (model B) | Polo like kinase 1
Structure information
PDB:4J52
PubMed:23664874
Release date:2013-05-29
Resolution:2.3 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 KIII.17 and EαC.24:Yes (2.7Å)
 
 
ASP rotation (xDFG.81) :353°
PHE rotation (xDFG.82) :12°
Activation loop position:-3.1Å
αC-helix position:17.8Å
 
G-rich loop angle:58.2°
G-rich loop distance:16.1Å
G-rich loop rotation:61.7°
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond protein
I2
H-bond protein
I3
H-bond protein
I4
H-bond protein
I5
H-bond ligand
H-bond protein
I11
H-bond ligand
H-bond protein
Binding pocket sequence
UniprotRFLGKGGFAKCFEFAGKIVKMSMEISIHRSLAQHVVGFHGFFVVLELCRRRSLLELHKRYLHRNRVIHRDLKLGNLFLIGDFGLA
Structure:RFLGKGGFAKCFEFAGKIVKMSMEISIHRSLAQHVVGFHGFFVVLELCRRRSLLELHKRYLHRNRVIHRDLKLGNLFLIGDFGLA


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: 1J3
Ligand Name: 4-{[(7R)-9-cyclopentyl-7-ethenyl-7-fluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl]amino}-3-methoxy-N-(4-methylpiperazin-1-yl)benzamide

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  • LABELS
  • KLIFS residue #
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  • COLORS
  • Interaction types
  • KLIFS (all res.)
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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
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

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Binding affinities
ChEMBL ID:CHEMBL2392544
Bioaffinities: 1 record for 1 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensSerine/threonine-protein kinase PLK18.58.58.5pIC501