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EGFR kinase (T790M/V948R) in complex with pf-06747775

Analyse EGFR kinase (T790M/V948R) in complex with pf-06747775 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JXI
Type: protein
Length: 1,136 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Epidermal growth factor receptor
EC: 2.7.10.1
UniProt: P00533
Ligands: 8BS
Pockets: 17 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	Epidermal growth factor receptor (EC 2.7.10.1)	protein	289	41% helix, 16% strand	P00533
A	Epidermal growth factor receptor (EC 2.7.10.1)	protein	290	44% helix, 17% strand	P00533
C	Epidermal growth factor receptor (EC 2.7.10.1)	protein	283	43% helix, 17% strand	P00533
B	Epidermal growth factor receptor (EC 2.7.10.1)	protein	274	42% helix, 18% strand	P00533

Ligands and binding sites

8BS · N-[(3R,4R)-4-fluoro-1-{6-[(3-methoxy-1-methyl-1H-pyrazol-4-yl)amino]-9-methyl-9H-purin-2-yl}pyrrolidin-3-yl]propanamide · ligand · 4 copies · chains D, A, C, B

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

Pockets

17 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	1103	0.80	0.81	78	empty
2	935	0.78	0.81	73	8BS
3	702	0.76	0.81	79	8BS
4	441	0.70	0.81	53	8BS
5	584	0.69	0.78	56	empty

Interfaces

5 interfaces between chains.

D–B · 772 Å² buried · 12 hydrogen bonds · protein-protein
D–A · 392 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 367 Å² buried · 1 hydrogen bond · protein-protein
A–B · 254 Å² buried · 0 hydrogen bonds · protein-protein
D–C · 184 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

7JXI · EGFR kinase (T790M/V948R) in complex with PF-06747775 · the same entry in another collection · chain B against B, TM-score 1.00
P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain B against A, TM-score 0.92

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 P00533
Elsewhere: RCSB PDB 7JXI · PDBe 7JXI · UniProt P00533

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