4ITH - chain B (model A) | Receptor interacting serine/threonine kinase 1
Structure information
PDB: | 4ITH |
PubMed: | 23473668 |
Release date: | 2013-03-13 |
Resolution: | 2.25 Å |
Kinase: | RIPK1 |
Family: | RIPK |
Group: | TKL |
Species: | HUMAN |
Quality Score: | 6 |
Missing Residues: | 6 |
Missing Atoms: | 16 |
DFG conformation: | out |
αC-helix conformation: | out |
Salt bridge KIII.17 and EαC.24: | No (12.4Å) |
ASP rotation (xDFG.81) : | 176° |
PHE rotation (xDFG.82) : | 175° |
Activation loop position: | 2Å |
αC-helix position: | 22.5Å |
G-rich loop angle: | - |
G-rich loop distance: | - |
G-rich loop rotation: | - |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond protein
Binding pocket sequence
Uniprot | AELDSGGFGKVSLMIMKTVALLEEAKMMNRLRSRVVKLLGVSLVMEYMEKGNLMHVLKAYLHGKGVIHKDLKPENILVIADLGLA |
Structure: | AEL______KVSLMIMKTVALLEEAKMMNRLRSRVVKLLGVSLVMEYMEKGNLMHVLKAYLHGKGVIHKDLKPENILVIADLGLA |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: RCM
Ligand Name: (5R)-5-[(7-chloro-1H-indol-3-yl)methyl]-3-methylimidazolidine-2,4-dione
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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 A 21 | 2 E 22 | 3 L 23 | 4 _ _ | 5 _ _ | 6 _ _ | 7 _ _ | 8 _ _ | 9 _ _ | 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 | |||||||||||||||
■▲ | ■ |
Binding affinities
ChEMBL ID:CHEMBL370438Bioaffinities: 4 records for 1 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Receptor-interacting serine/threonine-protein kinase 1 | 7.8 | 7.8 | 7.8 | pEC50 | 1 |
Homo sapiens | Receptor-interacting serine/threonine-protein kinase 1 | 6.5 | 6.2 | 6.7 | pIC50 | 3 |