5WNI - chain A | Receptor-interacting serine-threonine kinase 4
Structure information
PDB:5WNI
PubMed:29706531
Release date:2018-05-09
Resolution:2.65 Å
 
Kinase:Ripk4 (ANKRD3)
Family:RIPK
Group:TKL
Species:MOUSE
 
Quality Score:7.1
Missing Residues:4
Missing Atoms:13
DFG conformation:in
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes (2.5Å)
 
 
ASP rotation (xDFG.81) :340°
PHE rotation (xDFG.82) :
Activation loop position:-3.3Å
αC-helix position:17.1Å
 
G-rich loop angle:-
G-rich loop distance:-
G-rich loop rotation:-
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond ligand
H-bond protein
Binding pocket sequence
UniprotEKVGSGGFGQVYKLAIKCSELLEEAKKMEMAKRYILPVYGIGLVMEYMETGSLEKLLASHCMSPPLLHLDLKPANILLISDFGLA
Structure:EKVGS____QVYKLAIKCSELLEEAKKMEMAKRYILPVYGIGLVMEYMETGSLEKLLASHCMSPPLLHLNLKPANILLISDFGLA


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: ATP
Ligand Name: ADENOSINE-5'-TRIPHOSPHATE

  • Download image
  • LABELS
  • KLIFS residue #
  • Amino Acid
  • None
  • COLORS
  • Interaction types
  • KLIFS (all res.)
  • KLIFS (interacting res.)
  • None
  • OTHER
  • Show/hide non-interacting res.
  • En/disable resizing interacting res.
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
26
2 K
27
3 V
28
4 G
29
5 S
30
6 _
_
7 _
_
8 _
_
9 _
_
10 Q
35
11 V
36
12 Y
37
13 K
38
14 L
48
15 A
49
16 I
50
17 K
51
18 C
52
19 S
53
20 E
65
αC b.l IV
21 L
66
22 L
67
23 E
68
24 E
69
25 A
70
26 K
71
27 K
72
28 M
73
29 E
74
30 M
75
31 A
76
32 K
77
33 R
79
34 Y
80
35 I
81
36 L
82
37 P
83
38 V
84
39 Y
85
40 G
86
IV V GK hinge linker αD αE
41 I
87
42 G
93
43 L
94
44 V
95
45 M
96
46 E
97
47 Y
98
48 M
99
49 E
100
50 T
101
51 G
102
52 S
103
53 L
104
54 E
105
55 K
106
56 L
107
57 L
108
58 A
109
59 S
110
60 H
133
αE VI c.l VII VIII x
61 C
134
62 M
135
63 S
136
64 P
137
65 P
138
66 L
139
67 L
140
68 H
141
69 L
142
70 N
143
71 L
144
72 K
145
73 P
146
74 A
147
75 N
148
76 I
149
77 L
150
78 L
151
79 I
159
80 S
160
DFG a.l
81 D
161
82 F
162
83 G
163
84 L
164
85 A
165

Interaction pattern search
Search KLIFS for kinase-ligand complexes with similar interaction patterns:
Specify the minimum similarity (0.00 no similarity, 1.00 identical)
Binding affinities
ChEMBL ID:CHEMBL14249
Bioaffinities: 8 records for 3 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensMAP kinase-activated protein kinase 25.24.95.6pIC503
Homo sapiensMitogen-activated protein kinase kinase kinase 75.65.65.6pKd1
Homo sapiensTyrosine-protein kinase JAK25.95.95.9pKd4