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EGFR(T790M/V948R) in complex with AZD9291 and DDC4002

Analyse EGFR(T790M/V948R) in complex with AZD9291 and DDC4002 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XL4
Type: protein
Length: 1,187 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: NQ1, Q6K, ANP, MG
Pockets: 19 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Epidermal growth factor receptor (EC 2.7.10.1)	protein	293	42% helix, 17% strand	P00533
B	Epidermal growth factor receptor (EC 2.7.10.1)	protein	292	43% helix, 17% strand	P00533
C	Epidermal growth factor receptor (EC 2.7.10.1)	protein	302	41% helix, 17% strand	P00533
D	Epidermal growth factor receptor (EC 2.7.10.1)	protein	300	41% helix, 18% strand	P00533

Ligands and binding sites

NQ1 · 10-benzyl-8-fluoro-5,10-dihydro-11H-dibenzo[b,e][1, 4]diazepin-11-one · ligand · 3 copies · chains A, B, D
Q6K · ~{N}-[2-[2-(dimethylamino)ethyl-methyl-amino]-4-methoxy-5-[[4-(1-methylindol-3-yl)pyrimidin-2-yl]amino]phenyl]propanamide · ligand · 2 copies · chains A, B
ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains C, D
MG · Magnesium ion · metal · chains D

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

Pockets

19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1104	0.82	0.83	90	ANP, NQ1
2	689	0.79	0.84	82	NQ1, Q6K
3	364	0.77	0.87	30	empty
4	335	0.77	0.87	29	empty
5	553	0.74	0.82	71	empty

Interfaces

5 interfaces between chains.

B–D · 1639 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 1630 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 378 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 364 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 71 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

6XL4 · EGFR(T790M/V948R) in complex with AZD9291 and DDC4002 · the same entry in another collection · chain D against D, TM-score 1.00
P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain A against A, TM-score 0.91

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 6XL4 · PDBe 6XL4 · UniProt P00533

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