5D7A - chain C | TRAF2 and NCK interacting kinase
Structure information
PDB:5D7A
PubMed:27562646
Release date:2016-08-17
Resolution:2.9 Å
 
Kinase:TNIK
Family:STE20
Group:STE
Species:HUMAN
 
Quality Score:7.2
Missing Residues:2
Missing Atoms:0
DFG conformation:in
αC-helix conformation:out
Salt bridge KIII.17 and EαC.24:Yes (3.2Å)
 
 
ASP rotation (xDFG.81) :344°
PHE rotation (xDFG.82) :318°
Activation loop position:-5Å
αC-helix position:20.2Å
 
G-rich loop angle:53.5°
G-rich loop distance:15.6Å
G-rich loop rotation:72.9°
Other models from this PDB:
2D & 3D views

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


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: 58C
Ligand Name: cis-4-{[2-(1H-benzimidazol-5-ylamino)quinazolin-8-yl]oxy}cyclohexanol

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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
29
2 L
30
3 V
31
4 G
32
5 N
33
6 G
34
7 T
35
8 Y
36
9 G
37
10 Q
38
11 V
39
12 Y
40
13 K
41
14 A
51
15 A
52
16 I
53
17 K
54
18 V
55
19 M
56
20 E
65
αC b.l IV
21 I
66
22 K
67
23 Q
68
24 E
69
25 I
70
26 N
71
27 M
72
28 L
73
29 K
74
30 K
75
31 Y
76
32 S
77
33 R
80
34 N
81
35 I
82
36 A
83
37 T
84
38 Y
85
39 Y
86
40 G
87
IV V GK hinge linker αD αE
41 A
88
42 W
102
43 L
103
44 V
104
45 M
105
46 E
106
47 F
107
48 C
108
49 G
109
50 A
110
51 G
111
52 S
112
53 V
113
54 T
114
55 D
115
56 L
116
57 I
117
58 K
118
59 N
119
60 H
143
αE VI c.l VII VIII x
61 L
144
62 H
145
63 Q
146
64 H
147
65 K
148
66 V
149
67 I
150
68 H
151
69 R
152
70 D
153
71 I
154
72 K
155
73 G
156
74 Q
157
75 N
158
76 V
159
77 L
160
78 L
161
79 L
169
80 V
170
DFG a.l
81 D
171
82 F
172
83 G
173
84 _
_
85 _
_

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Binding affinities
Ligand not found in ChEMBL.