5WNK - chain A | Receptor-interacting serine-threonine kinase 4
Structure information
PDB:5WNK
PubMed:29706531
Release date:2018-05-09
Resolution:3.11 Å
 
Kinase:Ripk4 (ANKRD3)
Family:RIPK
Group:TKL
Species:MOUSE
 
Quality Score:7.2
Missing Residues:2
Missing Atoms:46
DFG conformation:in
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes (2.9Å)
 
 
ASP rotation (xDFG.81) :342°
PHE rotation (xDFG.82) :
Activation loop position:-3.4Å
αC-helix position:17.6Å
 
G-rich loop angle:-
G-rich loop distance:-
G-rich loop rotation:-
2D & 3D views

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


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: B6J
Ligand Name: 3,3'-(2,4-diaminopteridine-6,7-diyl)diphenol

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  • LABELS
  • KLIFS residue #
  • Amino Acid
  • None
  • 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 E
26
2 K
27
3 V
28
4 G
29
5 S
30
6 _
_
7 _
_
8 F
33
9 G
34
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
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Binding affinities
ChEMBL ID:CHEMBL230011
Bioaffinities: 114 records for 74 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensAdaptor-associated kinase5.55.56.1pKd2
Homo sapiensBMP-2-inducible protein kinase4.94.96.2pKd2
Homo sapiensBR serine/threonine-protein kinase 16.16.16.1pKd1
Homo sapiensBR serine/threonine-protein kinase 25.95.95.9pKd1
Homo sapiensCasein kinase I alpha6.16.16.1pKd1
Homo sapiensCasein kinase I delta5.95.95.9pKd1
Homo sapiensCasein kinase I epsilon5.95.95.9pKd1
Homo sapiensCasein kinase I gamma 15.25.25.2pKd1
Homo sapiensCasein kinase I gamma 25.65.65.6pKd1
Homo sapiensCasein kinase II alpha5.65.65.6pKd1
Homo sapiensCasein kinase II alpha (prime)5.85.85.8pKd1
Homo sapiensCasein kinase I isoform alpha-like5.75.75.7pKd1
Homo sapiensCasein kinase I isoform gamma-35.15.15.1pKd1
Homo sapiensChaperone activity of bc1 complex-like, mitochondrial777pKd1
Homo sapiensDual specificity mitogen-activated protein kinase kinase 35.25.25.2pKd1
Homo sapiensDual specificity mitogen-activated protein kinase kinase 45.45.45.4pKd1
Homo sapiensDual specificity protein kinase CLK27.47.47.4pKd1
Homo sapiensDual specificity protein kinase CLK35.25.25.2pKd1
Homo sapiensDual specificity protein kinase CLK46.96.96.9pKd1
Homo sapiensDual specificity protein kinase TTK5.15.15.1pKd1
Homo sapiensDual-specificity tyrosine-phosphorylation regulated kinase 1A6.26.26.2pKd1
Homo sapiensDual specificity tyrosine-phosphorylation-regulated kinase 1B6.16.16.1pKd1
Homo sapiensDual-specificity tyrosine-phosphorylation regulated kinase 25.35.35.3pKd1
Homo sapiensDual specificty protein kinase CLK16.96.96.9pKd1
Homo sapiensEpidermal growth factor receptor erbB15.75.16.1pKd12
Homo sapiensG protein-coupled receptor kinase 45.25.25.2pKd1
Homo sapiensMAP kinase-interacting serine/threonine-protein kinase MNK16.16.16.1pKd1
Homo sapiensMAP kinase signal-integrating kinase 26.16.16.1pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase 15.65.65.6pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase 75.65.65.6pKd1
Homo sapiensPhosphatidylinositol-4-phosphate 3-kinase C2 domain-containing beta polypeptide8.18.18.1pKd1
Homo sapiensPhosphatidylinositol-4-phosphate 3-kinase C2 domain-containing subunit gamma8.58.58.5pKd1
Homo sapiensPhosphatidylinositol-4-phosphate 5-kinase type-1 alpha5.85.85.8pKd1
Homo sapiensPhosphatidylinositol-4-phosphate 5-kinase type-1 gamma6.56.56.5pKd1
Homo sapiensPhosphatidylinositol-5-phosphate 4-kinase type-2 alpha5.25.25.2pKd1
Homo sapiensPhosphatidylinositol-5-phosphate 4-kinase type-2 beta5.15.15.1pKd1
Homo sapiensPhosphatidylinositol-5-phosphate 4-kinase type-2 gamma6.36.36.3pKd1
Homo sapiensPI3-kinase p110-alpha subunit5.95.95.9pIC502
Homo sapiensPI3-kinase p110-alpha subunit76.57.2pKd10
Homo sapiensPI3-kinase p110-beta subunit5.95.95.9pIC502
Homo sapiensPI3-kinase p110-beta subunit7.17.17.1pKd1
Homo sapiensPI3-kinase p110-delta subunit6.66.66.6pIC502
Homo sapiensPI3-kinase p110-delta subunit6.66.66.6pKd1
Homo sapiensPI3-kinase p110-gamma subunit7.17.17.1pIC502
Homo sapiensPI3-kinase p110-gamma subunit8.38.38.3pKd1
Homo sapiensPI4-kinase beta subunit6.46.46.4pKd1
Homo sapiensProtein kinase C nu6.16.16.1pKd1
Homo sapiensReceptor-interacting serine/threonine-protein kinase 35.45.45.4pKd1
Homo sapiensReceptor-interacting serine/threonine-protein kinase 4777pKd1
Homo sapiensReceptor protein-tyrosine kinase erbB-26.46.46.4pKd1
Homo sapiensReceptor protein-tyrosine kinase erbB-45.75.75.7pKd1
Homo sapiensRibosomal protein S6 kinase alpha 16.76.76.7pKd2
Homo sapiensRibosomal protein S6 kinase alpha 6666pKd2
Homo sapiensSerine/threonine-protein kinase 166.36.36.3pKd1
Homo sapiensSerine/threonine-protein kinase B-raf5.75.75.7pKd2
Homo sapiensSerine/threonine-protein kinase GAK5.95.95.9pKd1
Homo sapiensSerine/threonine-protein kinase LATS15.45.45.4pKd1
Homo sapiensSerine/threonine-protein kinase LATS25.85.85.8pKd1
Homo sapiensSerine/threonine-protein kinase mTOR6.26.26.2pKd1
Homo sapiensSerine/threonine-protein kinase Nek15.45.45.4pKd1
Homo sapiensSerine/threonine-protein kinase OSR15.65.65.6pKd1
Homo sapiensSerine/threonine-protein kinase RIO15.25.25.2pKd1
Homo sapiensSerine/threonine-protein kinase RIO25.85.85.8pKd1
Homo sapiensSerine/threonine-protein kinase RIPK25.75.76.3pKd2
Homo sapiensSerine/threonine-protein kinase SRPK15.35.35.3pKd1
Homo sapiensSerine/threonine-protein kinase SRPK3555pKd1
Homo sapiensSerine/threonine-protein kinase TAO16.36.36.3pKd1
Homo sapiensSerine/threonine-protein kinase TAO35.65.65.6pKd1
Homo sapiensSerine/threonine-protein kinase TNNI3K5.95.95.9pKd1
Homo sapiensSPS1/STE20-related protein kinase YSK45.45.45.4pKd1
Homo sapiensTransient receptor potential cation channel subfamily M member 68.18.18.1pKd1
Homo sapiensTyrosine-protein kinase ABL5.35.16.1pKd5
Homo sapiensTyrosine-protein kinase BRK5.35.35.3pKd1
Homo sapiensTyrosine-protein kinase JAK16.26.26.2pKd2
Homo sapiensTyrosine-protein kinase LCK5.55.55.5pKd1
Homo sapiensTyrosine-protein kinase receptor FLT37.47.47.4pKd1
Homo sapiensTyrosine-protein kinase TYK26.16.16.1pKd2
Homo sapiensUncharacterized aarF domain-containing protein kinase 45.95.95.9pKd1