6C4D - chain A | Receptor interacting serine/threonine kinase 1
Structure information
PDB:6C4D
PubMed:29485864
Release date:2018-03-21
Resolution:2.52 Å
 
Kinase:RIPK1
Family:RIPK
Group:TKL
Species:HUMAN
 
Quality Score:5.6
Missing Residues:6
Missing Atoms:0
DFG conformation:out
αC-helix conformation:out
Salt bridge KIII.17 and EαC.24:No (16.6Å)
 
 
ASP rotation (xDFG.81) :182°
PHE rotation (xDFG.82) :167°
Activation loop position:2.2Å
αC-helix position:22.6Å
 
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
No waters were found in the defined clusters
Binding pocket sequence
UniprotAELDSGGFGKVSLMIMKTVALLEEAKMMNRLRSRVVKLLGVSLVMEYMEKGNLMHVLKAYLHGKGVIHKDLKPENILVIADLGLA
Structure:______GFGKVSLMIMKTVALLEEAKMMNRLRSRVVKLLGVSLVMEYMEKGNLMHVLKAYLHGKGVIHKDLKPENILVIADLGLA


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: EJP
Ligand Name: (3S)-3-(2-benzyl-3-chloro-7-oxo-2,4,5,7-tetrahydro-6H-pyrazolo[3,4-c]pyridin-6-yl)-5-methyl-4-oxo-2,3,4,5-tetrahydro-1,5-benzoxazepine-8-carbonitrile

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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 _
_
2 _
_
3 _
_
4 _
_
5 _
_
6 _
_
7 G
27
8 F
28
9 G
29
10 K
30
11 V
31
12 S
32
13 L
33
14 M
42
15 I
43
16 M
44
17 K
45
18 T
46
19 V
47
20 A
59
αC b.l IV
21 L
60
22 L
61
23 E
62
24 E
63
25 A
64
26 K
65
27 M
66
28 M
67
29 N
68
30 R
69
31 L
70
32 R
71
33 S
73
34 R
74
35 V
75
36 V
76
37 K
77
38 L
78
39 L
79
40 G
80
IV V GK hinge linker αD αE
41 V
81
42 S
89
43 L
90
44 V
91
45 M
92
46 E
93
47 Y
94
48 M
95
49 E
96
50 K
97
51 G
98
52 N
99
53 L
100
54 M
101
55 H
102
56 V
103
57 L
104
58 K
105
59 A
106
60 Y
128
αE VI c.l VII VIII x
61 L
129
62 H
130
63 G
131
64 K
132
65 G
133
66 V
134
67 I
135
68 H
136
69 K
137
70 D
138
71 L
139
72 K
140
73 P
141
74 E
142
75 N
143
76 I
144
77 L
145
78 V
146
79 I
154
80 A
155
DFG a.l
81 D
156
82 L
157
83 G
158
84 L
159
85 A
160

Interaction pattern search
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Binding affinities
ChEMBL ID:CHEMBL4100398
Bioaffinities: 4 records for 2 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensReceptor-interacting serine/threonine-protein kinase 18.98.98.9pIC501
Homo sapiensReceptor-interacting serine/threonine-protein kinase 1999pKi1
Mus musculusReceptor-interacting serine/threonine-protein kinase 18.68.68.6pIC501
Mus musculusReceptor-interacting serine/threonine-protein kinase 17.17.17.1pKi1