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Aminopyrrolidine factor xa inhibitor

Analyse Aminopyrrolidine factor xa inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VWO
Type: protein
Length: 276 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Activated factor xa heavy chain; Factor X light chain
EC: 3.4.21.6
UniProt: P00742
Ligands: LZG, NA, CA, CL
Pockets: 2 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Activated factor xa heavy chain (EC 3.4.21.6)	protein	234	14% helix, 36% strand	P00742
L	Factor X light chain (EC 3.4.21.6)	protein	42	10% helix, 19% strand	P00742

Ligands and binding sites

LZG · 5-chloro-thiophene-2-carboxylic acid ((3S,4S)-4-fluoro- 1-{[2-fluoro-4-(2-oxo-2H-pyridin-1-yl)-phenylcarbamoyl]-methyl}-pyrrolidin-3-yl)-amide · ligand · chains A
NA · Sodium ion · metal · 3 copies · chains A
CA · Calcium ion · metal · chains A
CL · Chloride ion · ion · 2 copies · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	133	0.47	0.78	27	LZG
2	152	0.46	0.76	27	empty

Interfaces

1 interface between chains.

A–L · 894 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

2VWO · Aminopyrrolidine Factor Xa inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
P00742 · AlphaFold monomer V2.0 prediction for coagulation factor X (P00742) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P00742
Elsewhere: RCSB PDB 2VWO · PDBe 2VWO · UniProt P00742

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