MolNFT v1 · #159990 · protein

The co-crystal structure of BRAF(V600E) with PHI1

6P7G · SERINE/THREONINE-protein kinase B-RAF: “The co-crystal structure of BRAF(V600E) with PHI1”. X-ray diffraction, 1 ligand (E7M), 10 pockets (best druggability 0.76). MolNFT v1 #159990 on GenesisL1: 3D structure, binding sites and…

PDB: 6P7G
Type: protein
Length: 1,039 residues
Chains: 4
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: E7M
Pockets: 10 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1)	protein	256	41% helix, 17% strand	P15056
B	SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1)	protein	273	41% helix, 17% strand	P15056
C	SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1)	protein	256	43% helix, 17% strand	P15056
D	SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1)	protein	254	41% helix, 17% strand	P15056

Ligands and binding sites

E7M · 3-[(imidazo[1,2-b]pyridazin-3-yl)ethynyl]-4-methyl-N-[4-({[2-(morpholin-4-yl)ethyl]amino}methyl)-3-(trifluoromethyl)phenyl]benzamide · ligand · 4 copies · chains A, B, C, D
NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains B

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

Pockets

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	897	0.76	0.79	81	E7M
2	644	0.76	0.81	72	E7M
3	447	0.72	0.82	50	E7M
4	370	0.71	0.83	39	E7M
5	54	0.63	0.94	20	empty

Interfaces

3 interfaces between chains.

A–B · 1203 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 561 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 259 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6P7G · The co-crystal structure of BRAF(V600E) with PHI1 · the same entry in another collection · chain D against D, 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 A against A, TM-score 0.95

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 P15056
Elsewhere: RCSB PDB 6P7G · PDBe 6P7G · UniProt P15056

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