MolNFT v1 · #157952 · protein

Cyclic gmp-AMP synthase in complex with compound 20 inhibitor: 7- hydroxy-N-[(2S)-1-hydroxypropan-2-yl]-5-PHENYLPYRAZOLO[1,5- A]PYRIMIDINE-3-carboxamide

6NFO: “Cyclic gmp-AMP synthase in complex with compound 20 inhibitor: 7…”. X-ray diffraction, 2 ligands (KKM, ZN), 7 pockets (best druggability 0.75). MolNFT v1 #157952 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6NFO
Type: protein
Length: 703 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclic gmp-AMP synthase
EC: 2.7.7.86
UniProt: Q8N884
Ligands: KKM, ZN
Pockets: 7 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclic gmp-AMP synthase (EC 2.7.7.86)	protein	347	44% helix, 17% strand	Q8N884
B	Cyclic gmp-AMP synthase (EC 2.7.7.86)	protein	356	43% helix, 17% strand	Q8N884

Ligands and binding sites

KKM · 7-hydroxy-N-[(2S)-1-hydroxypropan-2-yl]-5-phenylpyrazolo[1,5-a]pyrimidine-3-carboxamide · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1059	0.75	0.77	101	KKM
2	810	0.74	0.78	64	KKM
3	258	0.59	0.79	31	empty
4	202	0.50	0.76	37	empty
5	91	0.37	0.76	24	empty

Interfaces

1 interface between chains.

A–B · 725 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

6NFO · CYCLIC GMP-AMP SYNTHASE in complex with compound 20 inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
Q8N884 · AlphaFold monomer V2.0 prediction for cyclic gmp-AMP synthase (Q8N884) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q8N884
Elsewhere: RCSB PDB 6NFO · PDBe 6NFO · UniProt Q8N884

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