5QCM | pdb_00005qcm

FACTOR XIA IN COMPLEX WITH THE INHIBITOR methyl ~{N}-[4-[[(1~{S})-2-[(~{E})-3-[3-chloranyl-2-fluoranyl-6-(1,2,3,4-tetrazol-1-yl)phenyl]prop-2-enoyl]-3,4-dihydro-1~{H}-isoquinolin-1-yl]carbonylamino]phenyl]carbamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.244 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5QCM

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Discovery of a Parenteral Small Molecule Coagulation Factor XIa Inhibitor Clinical Candidate (BMS-962212).

Pinto, D.J.P.Orwat, M.J.Smith, L.M.Quan, M.L.Lam, P.Y.S.Rossi, K.A.Apedo, A.Bozarth, J.M.Wu, Y.Zheng, J.J.Xin, B.Toussaint, N.Stetsko, P.Gudmundsson, O.Maxwell, B.Crain, E.J.Wong, P.C.Lou, Z.Harper, T.W.Chacko, S.A.Myers, J.E.Sheriff, S.Zhang, H.Hou, X.Mathur, A.Seiffert, D.A.Wexler, R.R.Luettgen, J.M.Ewing, W.R.

(2017) J Med Chem 60: 9703-9723

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b01171
  • Primary Citation Related Structures: 
    5QCK, 5QCL, 5QCM, 5QCN

  • PubMed Abstract: 

    Factor XIa (FXIa) is a blood coagulation enzyme that is involved in the amplification of thrombin generation. Mounting evidence suggests that direct inhibition of FXIa can block pathologic thrombus formation while preserving normal hemostasis. Preclinical studies using a variety of approaches to reduce FXIa activity, including direct inhibitors of FXIa, have demonstrated good antithrombotic efficacy without increasing bleeding. On the basis of this potential, we targeted our efforts at identifying potent inhibitors of FXIa with a focus on discovering an acute antithrombotic agent for use in a hospital setting. Herein we describe the discovery of a potent FXIa clinical candidate, 55 (FXIa K i = 0.7 nM), with excellent preclinical efficacy in thrombosis models and aqueous solubility suitable for intravenous administration. BMS-962212 is a reversible, direct, and highly selective small molecule inhibitor of FXIa.


  • Organizational Affiliation
    • Research and Development, Bristol-Myers Squibb Company , P.O. Box 5400, Princeton, New Jersey 08543, United States.

Macromolecule Content 

  • Total Structure Weight: 29.2 kDa 
  • Atom Count: 2,106 
  • Modeled Residue Count: 238 
  • Deposited Residue Count: 244 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Coagulation factor XI244Homo sapiensMutation(s): 0 
Gene Names: F11
EC: 3.4.21.27
UniProt & NIH Common Fund Data Resources
Find proteins for P03951 (Homo sapiens)
Explore P03951 
Go to UniProtKB:  P03951
PHAROS:  P03951
GTEx:  ENSG00000088926 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03951
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BVJ

Query on BVJ



Download:Ideal Coordinates CCD File
B [auth A]methyl ~{N}-[4-[[(1~{S})-2-[(~{E})-3-[3-chloranyl-2-fluoranyl-6-(1,2,3,4-tetrazol-1-yl)phenyl]prop-2-enoyl]-3,4-dihydro-1~{H}-isoquinolin-1-yl]carbonylamino]phenyl]carbamate
C28 H23 Cl F N7 O4
VNRXJEHYEMPJMV-ITMPFJHPSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.244 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.1α = 90
b = 79.1β = 90
c = 106.3γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2017-11-08 
  • Deposition Author(s): Sheriff, S.

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-08
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Database references
  • Version 1.2: 2018-02-21
    Changes: Structure summary
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Structure summary
  • Version 1.4: 2026-02-18
    Changes: Refinement description