5VUB - chain B (model A) | Pim-1 proto-oncogene, serine/threonine kinase
Structure information
PDB:5VUB
PubMed:29111719
Release date:2017-12-13
Resolution:2 Å
 
Kinase:PIM1
Family:PIM
Group:CAMK
Species:HUMAN
 
Quality Score:7.6
Missing Residues:1
Missing Atoms:0
DFG conformation:in
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes (2.4Å)
 
 
ASP rotation (xDFG.81) :341°
PHE rotation (xDFG.82) :
Activation loop position:-3.9Å
αC-helix position:17.9Å
 
G-rich loop angle:57.4°
G-rich loop distance:17.7Å
G-rich loop rotation:45.2°
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
I4
H-bond protein
I5
H-bond ligand
H-bond protein
I7
No H-bonds
Binding pocket sequence
UniprotPLLGSGGFGSVYSVAIKHVRVPMEVVLLKKVSSGVIRLLDWVLILERPEVQDLFDFITEHCHNCGVLHRDIKDENILILIDFGSG
Structure:PLLGSGGFGSVYSVAIKHVRVPMEVVLLKKVSSGVIRLLDWVLILERPEVQDLFDFITEHCHN_GVLHRDIKDENILILIDFGSG


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: 8GU
Ligand Name: (2Z)-6-methoxy-7-(piperazin-1-ylmethyl)-2-(1H-pyrrolo[3,2-b]pyridin-3-ylmethylidene)-1-benzofuran-3-one

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  • LABELS
  • KLIFS residue #
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  • COLORS
  • Interaction types
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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 P
42
2 L
43
3 L
44
4 G
45
5 S
46
6 G
47
7 G
48
8 F
49
9 G
50
10 S
51
11 V
52
12 Y
53
13 S
54
14 V
64
15 A
65
16 I
66
17 K
67
18 H
68
19 V
69
20 R
85
αC b.l IV
21 V
86
22 P
87
23 M
88
24 E
89
25 V
90
26 V
91
27 L
92
28 L
93
29 K
94
30 K
95
31 V
96
32 S
97
33 S
101
34 G
102
35 V
103
36 I
104
37 R
105
38 L
106
39 L
107
40 D
108
IV V GK hinge linker αD αE
41 W
109
42 V
117
43 L
118
44 I
119
45 L
120
46 E
121
47 R
122
48 P
123
49 E
124
50 V
126
51 Q
127
52 D
128
53 L
129
54 F
130
55 D
131
56 F
132
57 I
133
58 T
134
59 E
135
60 H
157
αE VI c.l VII VIII x
61 C
158
62 H
159
63 N
160
64 _
_
65 G
162
66 V
163
67 L
164
68 H
165
69 R
166
70 D
167
71 I
168
72 K
169
73 D
170
74 E
171
75 N
172
76 I
173
77 L
174
78 I
175
79 L
184
80 I
185
DFG a.l
81 D
186
82 F
187
83 G
188
84 S
189
85 G
190

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Binding affinities
ChEMBL ID:CHEMBL2147770
Bioaffinities: 2 records for 1 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensSerine/threonine-protein kinase PIM16.46.46.4pIC502