1MQ5

Crystal Structure of 3-chloro-N-[4-chloro-2-[[(4-chlorophenyl)amino]carbonyl]phenyl]-4-[(4-methyl-1-piperazinyl)methyl]-2-thiophenecarboxamide Complexed with Human Factor Xa

Structural Biology Knowledgebase: 1MQ5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.190

Literature

Macromolecules
Sequence Display for 1MQ5

Classification: BLOOD CLOTTING

Total Structure Weight: 32660.56

Macromolecule Entities
Molecule Chains Length Organism Details
COAGULATION FACTOR X HEAVY CHAIN A 233 Homo sapiens EC#: 3.4.21.6 IUBMB
Fragment: CATALYTIC DOMAIN
Gene Name(s): F10 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
COAGULATION FACTOR X LIGHT CHAIN L 51 Homo sapiens EC#: 3.4.21.6 IUBMB
Fragment: EPIDERMAL GROWTH FACTOR LIKE DOMAIN 2
Gene Name(s): F10 Gene View

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
XLC
Query on XLC

A 3-CHLORO-N-[4-CHLORO-2-[[(4-CHLOROPHENYL)AMINO]CARBONYL]PHENYL]- 4-[(4-METHYL-1-PIPERAZINYL)METHYL]-2-THIOPHENECARBOXAMIDE
C24 H23 Cl3 N4 O2 S
FIZKTFMGWNHPMZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, L GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
XLC Ki: 0.76 - 1 nM (100) BindingDB

Ki: 1 nM  BindingMOAD
Ki: 1 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.190
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 56.36 α = 90.00
b = 72.02 β = 90.00
c = 78.92 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-09-13
  • Released Date: 2003-01-28
  • Deposition author(s): Adler, M., Whitlow, M.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update