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Crystal structure of inactive KRAS G12D (GDP) in complex with the soaked dimeric inhibitor bi-5747

Analyse Crystal structure of inactive KRAS G12D (GDP) in complex with the soaked… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ACQ
Type: protein
Length: 487 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTPase KRAS
EC: 3.6.5.2
UniProt: P01116
Ligands: GDP, R6W, MG
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTPase KRAS (EC 3.6.5.2)	protein	164	38% helix, 26% strand	P01116
B	GTPase KRAS (EC 3.6.5.2)	protein	163	37% helix, 25% strand	P01116
C	GTPase KRAS (EC 3.6.5.2)	protein	160	38% helix, 26% strand	P01116

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
R6W · (3~{S})-5-oxidanyl-3-[2-[[6-[[3-[(1~{S})-6-oxidanyl-3-oxidanylidene-1,2-dihydroisoindol-1-yl]-1~{H}-indol-2-yl]methylamino]hexylamino]methyl]-1~{H}-indol-3-yl]-2, 3-dihydroisoindol-1-one · ligand · 2 copies · chains A, B, C
MG · Magnesium ion · metal · 3 copies · chains A, B, C

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	616	0.69	0.78	55	R6W
2	151	0.54	0.80	22	empty
3	138	0.48	0.78	27	GDP, MG
4	118	0.44	0.77	26	GDP, MG
5	118	0.42	0.76	27	GDP, MG

Interfaces

3 interfaces between chains.

B–C · 286 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 212 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 17 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7ACQ · Crystal structure of inactive KRAS G12D (GDP) in complex with the soaked dimeric… · the same entry in another collection · chain A against A, TM-score 1.00

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 P01116
Elsewhere: RCSB PDB 7ACQ · PDBe 7ACQ · UniProt P01116

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