› 4x6n

X-ray diffraction
2.1Å resolution

FACTOR XIA IN COMPLEX WITH THE INHIBITOR 1-{(1S)-1-[4-(3-amino-1H-indazol-6-yl)-5-chloro-1H-imidazol-2-yl]-2-phenylethyl}-3-[5-chloro-2-(1H-tetrazol-1-yl)benzyl]urea

Released:
DOI: 10.2210/pdb4x6n/pdb
PDB entry 4x6n coloured by chain, front view.
PDB entry 4x6n coloured by chain, side view.
PDB entry 4x6n coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-based design of inhibitors of coagulation factor XIa with novel P1 moieties.
Pinto DJ, Smallheer JM, Corte JR, Austin EJ, Wang C, Fang T, Smith LM, Rossi KA, Rendina AR, Bozarth JM, Zhang G, Wei A, Ramamurthy V, Sheriff S, Myers JE, Morin PE, Luettgen JM, Seiffert DA, Quan ML, Wexler RR
Bioorg Med Chem Lett 25 1635-42 (2015)
PMID: 25728130

Function and Biology Details

Reaction catalysed: 
Selective cleavage of Arg-|-Ala and Arg-|-Val bonds in factor IX to form factor IXa.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-137279 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Coagulation factor XIa light chain Chain: A
Molecule details ›
Chain: A
Length: 244 amino acids
Theoretical weight: 27.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P03951 (Residues: 388-625; Coverage: 39%)
Gene name: F11
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Coagulation factor XIa heavy chain Chain: H
Molecule details ›
Chain: H
Length: 18 amino acids
Theoretical weight: 2.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P03951 (Residues: 375-387; Coverage: 2%)
Gene name: F11

Ligands and Environments

3 bound ligands:
Ligand 3Y5 1 x 3Y5
Ligand SO4 1 x SO4
Ligand EDO 11 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E SUPERBRIGHT
Spacegroup: P3221
Unit cell:
a: 79.1Å b: 79.1Å c: 105.9Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.175 0.171 0.21
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Harnessing the cyclization strategy for new drug discovery.
Tang et al. (2022)
1 more

1 mention without citation

ArkDTA: attention regularization guided by non-covalent interactions for explainable drug-target binding affinity prediction.
Gim et al. (2023)