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
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
Uniprot | EFVGKGGFGVVFRVAVKIVKISWEVKAMVNLRENVLLLLGVALVTRFMENGSLAGLLQPHSLNPPLLHRDLKPSNILLLADFGLS |
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
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- 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 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 | |||||||||||||||
Binding affinities
ChEMBL ID:CHEMBL1230989Bioaffinities: No (p)Ki/(p)IC50/(p)EC50 values for kinases found (with a ChEMBL confidence ≥ 8).