MolNFT v1 · #144782 · protein
Structure based design of RIP1 kinase inhibitors
6C4D · Receptor-interacting SERINE/THREONINE-protein kinase 1: “Structure based design of RIP1 kinase inhibitors”. X-ray diffraction, 1 ligand (EJP), 16 pockets (best druggability 0.76). MolNFT v1 #144782 on GenesisL1: 3D structure…
- PDB
- 6C4D
- Type
- protein
- Length
- 1,057 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-interacting SERINE/THREONINE-protein kinase 1
- EC
- 2.7.11.1
- UniProt
- Q13546
- Ligands
- EJP
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 267 | 41% helix, 15% strand | Q13546 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 266 | 43% helix, 18% strand | Q13546 |
| C | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 258 | 40% helix, 15% strand | Q13546 |
| D | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 266 | 37% helix, 15% strand | Q13546 |
Ligands and binding sites
- EJP · (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 · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.76 | 0.89 | 37 | EJP |
| 2 | 872 | 0.76 | 0.79 | 85 | empty |
| 3 | 304 | 0.75 | 0.87 | 32 | EJP |
| 4 | 256 | 0.73 | 0.87 | 35 | EJP |
| 5 | 346 | 0.72 | 0.84 | 39 | EJP |
Interfaces
4 interfaces between chains.
- A–C · 451 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 254 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 163 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 131 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q13546
- Elsewhere: RCSB PDB 6C4D · PDBe 6C4D · UniProt Q13546
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