5ZXB - chain B (model B) | Tyrosine kinase, non-receptor, 2
Structure information
PDB:5ZXB
PubMed:30153003
Release date:2018-09-26
Resolution:2.2 Å
 
Kinase:TNK2 (ACK)
Family:Ack
Group:TK
Species:HUMAN
 
Quality Score:5.2
Missing Residues:7
Missing Atoms:0
DFG conformation:out
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes (2.7Å)
 
 
ASP rotation (xDFG.81) :192°
PHE rotation (xDFG.82) :181°
Activation loop position:2.4Å
αC-helix position:19.1Å
 
G-rich loop angle:-
G-rich loop distance:-
G-rich loop rotation:-
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
O1
H-bond ligand
Binding pocket sequence
UniprotEKLGDGSFGVVRRVAVKCLDFIREVNAMHSLDRNLIRLYGVKMVTELAPLGSLLDRLRKYLESKRFIHRDLAARNLLLIGDFGLM
Structure:EKLGD____VVRRVAVKCLDFIREVNAMHSLDRNLIRLYGVKMVTELAPLGSLLDRLRKYLESKRFIHRDLAARNLLLIGDF___


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: 9KO
Ligand Name: N-{3-[7-{[6-(4-acetylpiperazin-1-yl)pyridin-3-yl]amino}-1-methyl-2-oxo-1,4-dihydropyrimido[4,5-d]pyrimidin-3(2H)-yl]-4-methylphenyl}-3-(trifluoromethyl)benzamide

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  • LABELS
  • KLIFS residue #
  • Amino Acid
  • None
  • COLORS
  • Interaction types
  • KLIFS (all res.)
  • KLIFS (interacting res.)
  • None
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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 E
130
2 K
131
3 L
132
4 G
133
5 D
134
6 _
_
7 _
_
8 _
_
9 _
_
10 V
139
11 V
140
12 R
141
13 R
142
14 V
155
15 A
156
16 V
157
17 K
158
18 C
159
19 L
160
20 D
173
αC b.l IV
21 F
174
22 I
175
23 R
176
24 E
177
25 V
178
26 N
179
27 A
180
28 M
181
29 H
182
30 S
183
31 L
184
32 D
185
33 R
187
34 N
188
35 L
189
36 I
190
37 R
191
38 L
192
39 Y
193
40 G
194
IV V GK hinge linker αD αE
41 V
195
42 K
202
43 M
203
44 V
204
45 T
205
46 E
206
47 L
207
48 A
208
49 P
209
50 L
210
51 G
211
52 S
212
53 L
213
54 L
214
55 D
215
56 R
216
57 L
217
58 R
218
59 K
219
60 Y
242
αE VI c.l VII VIII x
61 L
243
62 E
244
63 S
245
64 K
246
65 R
247
66 F
248
67 I
249
68 H
250
69 R
251
70 D
252
71 L
253
72 A
254
73 A
255
74 R
256
75 N
257
76 L
258
77 L
259
78 L
260
79 I
268
80 G
269
DFG a.l
81 D
270
82 F
271
83 _
_
84 _
_
85 _
_

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Binding affinities
ChEMBL ID:CHEMBL4214342
Bioaffinities: 2 records for 2 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 2999pIC501
Homo sapiensTyrosine kinase non-receptor protein 28.18.18.1pIC501