MolNFT v1 · #106324 · protein
MAP4K4 in complex with a pyridin-2(1H)-one derivative
4RVT · Mitogen-activated protein kinase kinase kinase kinase 4: “MAP4K4 in complex with a pyridin-2(1H)-one derivative”. X-ray diffraction, 1 ligand (3XM), 6 pockets (best druggability 0.79). MolNFT v1 #106324 on GenesisL1: 3D structure…
- PDB
- 4RVT
- Type
- protein
- Length
- 578 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase kinase kinase kinase 4
- EC
- 2.7.11.1
- UniProt
- O95819
- Ligands
- 3XM
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase kinase kinase kinase 4 (EC 2.7.11.1) | protein | 281 | 38% helix, 16% strand | O95819 |
| B | Mitogen-activated protein kinase kinase kinase kinase 4 (EC 2.7.11.1) | protein | 297 | 38% helix, 17% strand | O95819 |
Ligands and binding sites
- 3XM · 3-hexanoyl-4-hydroxy-5-(4-hydroxyphenyl)pyridin-2(1H)-one · ligand · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.79 | 0.80 | 109 | empty |
| 2 | 249 | 0.70 | 0.86 | 35 | 3XM |
| 3 | 221 | 0.59 | 0.80 | 23 | empty |
| 4 | 67 | 0.52 | 0.86 | 23 | empty |
| 5 | 56 | 0.42 | 0.82 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1413 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4RVT · MAP4K4 in complex with a pyridin-2(1H)-one derivative · the same entry in another collection · chain A against A, TM-score 1.00
- O95819 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase kinase kinase… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 O95819
- Elsewhere: RCSB PDB 4RVT · PDBe 4RVT · UniProt O95819
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