MolNFT v1 · #135691 · protein

Factor viia in complex with the inhibitor 3-{[(2R)-17-ethyl-4-methyl- 3,12-dioxo-7-[(propan-2-YL)SULFONYL]-13-oxa-4,11- DIAZATRICYCLO[14.2.2.1~6,10~]HENICOSA-1(18),6(21),7,9,16,19-hexaen-2- YL]AMINO}BENZAMIDE

5U6J · Coagulation factor VII heavy chain: “Factor viia in complex with the inhibitor 3-{[(2R)-17-ethyl-4-methyl…”. X-ray diffraction, 3 ligands (82J, CA, SO4), 3 pockets (best druggability 0.43). MolNFT v1 #135691 on GenesisL1: 3D…

PDB: 5U6J
Type: protein
Length: 306 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coagulation factor VII heavy chain; Coagulation factor VII light chain
EC: 3.4.21.21
UniProt: P08709
Ligands: 82J, CA, SO4
Pockets: 3 · best druggability 0.43

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Coagulation factor VII heavy chain (EC 3.4.21.21)	protein	251	15% helix, 37% strand	P08709
L	Coagulation factor VII light chain (EC 3.4.21.21)	protein	55	15% helix, 25% strand	P08709

Ligands and binding sites

82J · 3-{[(2R)-17-ethyl-4-methyl-3,12-dioxo-7-[(propan-2-yl) sulfonyl]-13-oxa-4,11-diazatricyclo[14.2.2.1~6, 10~]henicosa-1(18),6(21),7,9,16,19-hexaen-2-yl]amino}benzamide · ligand · chains H
CA · Calcium ion · metal · chains H
SO4 · Sulfate ion · ion · 4 copies · chains H, L
GOL · Glycerol · additive · 2 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	63	0.43	0.82	16	SO4
2	130	0.41	0.75	29	82J
3	90	0.36	0.75	18	SO4

Interfaces

1 interface between chains.

H–L · 1018 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5U6J · Factor VIIa in complex with the inhibitor 3-{[(2R)-17-ethyl-4-methyl-3,12-dioxo-7-[(propan… · 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 5U6J · PDBe 5U6J · UniProt P08709

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