4M69 - chain A (model B) | Receptor-interacting serine-threonine kinase 3
Structure information
PDB:4M69
PubMed:24095729
Release date:2013-10-16
Resolution:2.5 Å
 
Kinase:Ripk3 (RIPK3)
Family:RIPK
Group:TKL
Species:MOUSE
 
Quality Score:8
Missing Residues:0
Missing Atoms:0
DFG conformation:in
αC-helix conformation:out
Salt bridge KIII.17 and EαC.24:No (16.7Å)
 
 
ASP rotation (xDFG.81) :321°
PHE rotation (xDFG.82) :326°
Activation loop position:-4.9Å
αC-helix position:20.9Å
 
G-rich loop angle:47°
G-rich loop distance:14Å
G-rich loop rotation:51.5°
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I3
H-bond protein
I4
No H-bonds
I5
H-bond protein
Binding pocket sequence
UniprotEFVGKGGFGVVFRVAVKIVKISWEVKAMVNLRENVLLLLGVALVTRFMENGSLAGLLQPHSLNPPLLHRDLKPSNILLLADFGLS
Structure:EFVGKGGFGVVFRVAVKIVKISWEVKAMVNLRENVLLLLGVALVTRFMENGSLAGLLQPHSLDPPLLHRDLKPSNILLLADFGLS


Modified residues
Residue 184 (not in pocket)
Phosphorylated serine
Residue 231 (not in pocket)
Phosphorylated threonine
Residue 232 (not in pocket)
Phosphorylated serine
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: ANP
Ligand Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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  • LABELS
  • KLIFS residue #
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  • 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
26
2 F
27
3 V
28
4 G
29
5 K
30
6 G
31
7 G
32
8 F
33
9 G
34
10 V
35
11 V
36
12 F
37
13 R
38
14 V
48
15 A
49
16 V
50
17 K
51
18 I
52
19 V
53
20 K
57
αC b.l IV
21 I
58
22 S
59
23 W
60
24 E
61
25 V
62
26 K
63
27 A
64
28 M
65
29 V
66
30 N
67
31 L
68
32 R
69
33 E
71
34 N
72
35 V
73
36 L
74
37 L
75
38 L
76
39 L
77
40 G
78
IV V GK hinge linker αD αE
41 V
79
42 A
92
43 L
93
44 V
94
45 T
95
46 R
96
47 F
97
48 M
98
49 E
99
50 N
100
51 G
101
52 S
102
53 L
103
54 A
104
55 G
105
56 L
106
57 L
107
58 Q
108
59 P
109
60 H
133
αE VI c.l VII VIII x
61 S
134
62 L
135
63 D
136
64 P
137
65 P
138
66 L
139
67 L
140
68 H
141
69 R
142
70 D
143
71 L
144
72 K
145
73 P
146
74 S
147
75 N
148
76 I
149
77 L
150
78 L
151
79 L
159
80 A
160
DFG a.l
81 D
161
82 F
162
83 G
163
84 L
164
85 S
165

Interaction pattern search
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Binding affinities
ChEMBL ID:CHEMBL1230989

Bioaffinities: No (p)Ki/(p)IC50/(p)EC50 values for kinases found (with a ChEMBL confidence ≥ 8).