GL1X · GenesisL1 explorer

MolNFT v1 · #136996 · protein

Braf in complex with RAF709

5VAM · SERINE/THREONINE-protein kinase B-RAF: “Braf in complex with RAF709”. X-ray diffraction, 1 ligand (92J), 4 pockets (best druggability 0.75). MolNFT v1 #136996 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
5VAM
Type
protein
Length
529 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
SERINE/THREONINE-protein kinase B-RAF
EC
2.7.11.1
UniProt
P15056
Ligands
92J
Pockets
4 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ASERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1)protein26941% helix, 17% strandP15056
BSERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1)protein26042% helix, 17% strandP15056

Ligands and binding sites

  • 92J · N-{2-methyl-5'-(morpholin-4-yl)-6'-[(oxan-4-yl)oxy][3, 3'-bipyridin]-5-yl}-3-(trifluoromethyl)benzamide · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
14330.750.845192J
23070.730.853592J
34770.720.8257empty
41480.550.8127empty

Interfaces

1 interface between chains.

  • A–B · 994 Ų buried · 15 hydrogen bonds · protein-protein

Compared structures

  • 5VAM · BRAF in Complex with RAF709 · the same entry in another collection · chain A against A, TM-score 1.00
  • P15056 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase B-RAF (P15056) · a predicted model of the same protein · chain B against A, TM-score 0.95

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