MolNFT v1 · #28508 · protein

Short factor viia with a small molecule inhibitor

1YGC · Coagulation factor VII: “Short factor viia with a small molecule inhibitor”. X-ray diffraction, 3 ligands (905, CA, SO4), 3 pockets (best druggability 0.49). MolNFT v1 #28508 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1YGC
Type: protein
Length: 307 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coagulation factor VII
EC: 3.4.21.21
UniProt: P08709
Ligands: 905, CA, SO4
Pockets: 3 · best druggability 0.49

Structure

x-ray diffraction · 2 distinct chains · 14% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Coagulation factor VII (EC 3.4.21.21)	protein	254	15% helix, 37% strand	P08709
L	Coagulation factor VII	protein	53	8% helix, 26% strand	P08709

Ligands and binding sites

905 · (R)-4-[2-(3-amino-benzenesulfonylamino)-1-(3,5-diethoxy-2-fluorophenyl)-2-oxo-ethylamino]-2-hydroxy-benzamidine · ligand · chains H
CA · Calcium ion · metal · 2 copies · chains H
SO4 · Sulfate ion · ion · 7 copies · chains H, L

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

Pockets

3 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	77	0.49	0.83	17	SO4
2	101	0.39	0.77	23	905
3	119	0.39	0.74	24	empty

Interfaces

1 interface between chains.

H–L · 1032 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1YGC · Short Factor VIIa with a small molecule inhibitor · the same entry in another collection · chain H against H, TM-score 1.00
P08709 · AlphaFold monomer V2.0 prediction for coagulation factor VII (P08709) · a predicted model of the same protein · chain H against A, TM-score 0.97

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 P08709
Elsewhere: RCSB PDB 1YGC · PDBe 1YGC · UniProt P08709

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