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B-RAF kinase in complex with BIRB796

Analyse B-RAF kinase in complex with BIRB796 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JVG
Type: protein
Length: 1,041 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: B96
Pockets: 13 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1)	protein	259	40% helix, 16% strand	P15056
A, D	SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1)	protein	262	39% helix, 17% strand	P15056
C	SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1)	protein	258	40% helix, 17% strand	P15056

Ligands and binding sites

B96 · 1-(5-tert-butyl-2-P-tolyl-2H-pyrazol-3-yl)-3-[4-(2-morpholin-4-yl-ethoxy)-naphthalen-1-yl]-urea · ligand · 4 copies · chains B, A, C, D

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

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	545	0.77	0.84	58	B96
2	530	0.77	0.84	55	B96
3	573	0.76	0.82	58	B96
4	497	0.71	0.81	47	B96
5	313	0.71	0.85	41	empty

Interfaces

5 interfaces between chains.

C–D · 1341 Å² buried · 16 hydrogen bonds · protein-protein
B–A · 1270 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 310 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 248 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 83 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

4JVG · B-Raf Kinase in Complex with Birb796 · 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 C against A, TM-score 0.94

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 4JVG · PDBe 4JVG · UniProt P15056

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