3KQD | pdb_00003kqd

Factor xa in complex with the inhibitor 1-(3-(5-oxo-4,5- dihydro-1h-1,2,4-triazol-3-yl)phenyl)-6-(2'-(pyrrolidin-1- ylmethyl)biphenyl-4-yl)-3-(trifluoromethyl)-5,6-dihydro- 1h-pyrazolo[3,4-c]pyridin-7(4h)-one

• PDB DOI: https://doi.org/10.2210/pdb3KQD/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2009-11-17 Released: 2010-02-23 
• Deposition Author(s): Sheriff, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.254 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Phenyltriazolinones as potent factor Xa inhibitors.

Quan, M.L., Pinto, D.J., Rossi, K.A., Sheriff, S., Alexander, R.S., Amparo, E., Kish, K., Knabb, R.M., Luettgen, J.M., Morin, P., Smallwood, A., Woerner, F.J., Wexler, R.R.

(2010) Bioorg Med Chem Lett 20: 1373-1377

• PubMed: 20100660 
• DOI: https://doi.org/10.1016/j.bmcl.2010.01.011
• Primary Citation Related Structures: 
  3FFG, 3KQB, 3KQC, 3KQD, 3KQE


• PubMed Abstract: 
  

  We have discovered that phenyltriazolinone is a novel and potent P1 moiety for coagulation factor Xa. X-ray structures of the inhibitors with a phenyltriazolinone in the P1 position revealed that the side chain of Asp189 has reoriented resulting in a novel S1 binding pocket which is larger in size to accommodate the phenyltriazolinone P1 substrate.

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Organizational Affiliation: 
• Research and Development, Bristol-Myers Squibb, PO Box 5400, Princeton, NJ 08543-5400, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.68 kDa 
• Atom Count: 2,282 
• Modeled Residue Count: 286 
• Deposited Residue Count: 286 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
factor Xa heavy chain	A	234	Homo sapiens	Mutation(s): 0  EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
PHAROS:  P00742 GTEx:  ENSG00000126218

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
factor Xa light chain	B [auth L]	52	Homo sapiens	Mutation(s): 0  EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
PHAROS:  P00742 GTEx:  ENSG00000126218

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LGL	C [auth A]	1-(3-(5-OXO-4,5-DIHYDRO-1H-1,2,4-TRIAZOL-3-YL)PHENYL)-6-(2'-(PYRROLIDIN-1-YLMETHYL)BIPHENYL-4-YL)-3-(TRIFLUOROMETHYL)-5,6-DIHYDRO-1H-PYRAZOLO[3,4-C]PYRIDIN-7(4H)-ONE C32 H28 F3 N7 O2 QNPOXJFBWDKXGC-UHFFFAOYSA-N
NA	D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.254 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.7	α = 90
b = 72.1	β = 90
c = 76.8	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-23 
Deposition Author(s): Sheriff, S.

Revision History  

• Version 1.0: 2010-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary