Research workbench
B-RAF V600E kinase domain in complex with an aminoisoquinoline inhibitor
Analyse B-RAF V600E kinase domain in complex with an aminoisoquinoline inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IDP
- Type
- protein
- Length
- 511 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B-RAF proto-oncogene SERINE/THREONINE-protein kinase
- EC
- 2.7.11.1
- UniProt
- P15056
- Ligands
- L1E
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | B-RAF proto-oncogene SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 256 | 39% helix, 16% strand | P15056 |
| A | B-RAF proto-oncogene SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 255 | 41% helix, 18% strand | P15056 |
Ligands and binding sites
- L1E · N~1~-(4-chlorophenyl)-6-methyl-N~5~-[3-(7H-purin-6-yl)pyridin-2-yl]isoquinoline-1,5-diamine · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.75 | 0.82 | 51 | L1E |
| 2 | 502 | 0.73 | 0.81 | 48 | L1E |
| 3 | 450 | 0.70 | 0.81 | 48 | empty |
Interfaces
1 interface between chains.
- B–A · 1114 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3IDP · B-Raf V600E kinase domain in complex with an aminoisoquinoline inhibitor · the same entry in another collection · chain B against B, 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 3IDP · PDBe 3IDP · UniProt P15056
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