3THB - chain A | Polo like kinase 1
Structure information
PDB:3THB
PubMed:22070629
Release date:2011-11-23
Resolution:2.5 Å
 
Kinase:PLK1
Family:PLK
Group:Other
Species:HUMAN
 
Quality Score:8
Missing Residues:0
Missing Atoms:21
DFG conformation:in
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes (3.5Å)
 
 
ASP rotation (xDFG.81) :339°
PHE rotation (xDFG.82) :
Activation loop position:-3.2Å
αC-helix position:18.3Å
 
G-rich loop angle:53.2°
G-rich loop distance:15.2Å
G-rich loop rotation:66.1°
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
No waters were found in the defined clusters
Binding pocket sequence
UniprotRFLGKGGFAKCFEFAGKIVKMSMEISIHRSLAQHVVGFHGFFVVLELCRRRSLLELHKRYLHRNRVIHRDLKLGNLFLIGDFGLA
Structure:RFLGKGGFAKCFEFAGKIVKMSMEISIHRSLAQHVVGFHGFFVVLELCRRRSLLELHKRYLHRNRVIHRDLKLGNLFLIGDFGLA


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: 3TA
Ligand Name: 9-chloro-2-({5-[3-(dimethylamino)propyl]-2-methylpyridin-3-yl}amino)-5,7-dihydro-6H-pyrimido[5,4-d][1]benzazepine-6-thione

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  • LABELS
  • KLIFS residue #
  • Amino Acid
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  • 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
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:CHEMBL1945804
Bioaffinities: 8 records for 7 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensFibroblast growth factor receptor 16.76.76.7pIC501
Homo sapiensPlatelet-derived growth factor receptor beta7.37.37.3pIC501
Homo sapiensSerine/threonine-protein kinase PLK14.54.54.5pEC501
Homo sapiensSerine/threonine-protein kinase PLK18.78.78.7pIC501
Homo sapiensSerine/threonine-protein kinase PLK37.27.27.2pIC501
Homo sapiensStem cell growth factor receptor6.26.26.2pIC501
Homo sapiensTyrosine-protein kinase receptor FLT36.16.16.1pIC501
Homo sapiensVascular endothelial growth factor receptor 26.96.96.9pIC501