6CYM

Reversible Covalent Direct Thrombin Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb6CYM/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2018-04-06 Released: 2018-05-09 
• Deposition Author(s): Sivaraja, M., Williams, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.254 
• R-Value Work: 0.176 
• R-Value Observed: 0.180 

Literature

Reversible covalent direct thrombin inhibitors.

Sivaraja, M., Pozzi, N., Rienzo, M., Lin, K., Shiau, T.P., Clemens, D.M., Igoudin, L., Zalicki, P., Chang, S.S., Estiarte, M.A., Short, K.M., Williams, D.C., Datta, A., Di Cera, E., Kita, D.B.

(2018) PLoS One 13: e0201377-e0201377

• PubMed: 30071045 
• DOI: https://doi.org/10.1371/journal.pone.0201377
• Primary Citation of Related Structures:  
  6CYM


• PubMed Abstract: 
  

  In recent years, the traditional treatments for thrombotic diseases, heparin and warfarin, are increasingly being replaced by novel oral anticoagulants offering convenient dosing regimens, more predictable anticoagulant responses, and less frequent monitoring. However, these drugs can be contraindicated for some patients and, in particular, their bleeding liability remains high.

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Organizational Affiliation: 

Verseon Corporation, Fremont, California, United States of America.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.74 kDa 
• Atom Count: 4,614 
• Modelled Residue Count: 562 
• Deposited Residue Count: 574 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	A, C	259	Homo sapiens	Mutation(s): 0  EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	B, D	28	Homo sapiens	Mutation(s): 0  EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
71F	E [auth A], H [auth C]	2-methoxybenzoic acid C8 H8 O3 ILUJQPXNXACGAN-UHFFFAOYSA-N
NA	G [auth A], I [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.254 
• R-Value Work: 0.176 
• R-Value Observed: 0.180 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.67	α = 90
b = 99.73	β = 90
c = 146.01	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-09 
Deposition Author(s): Sivaraja, M., Williams, D.C.

Revision History  

• Version 1.0: 2018-05-09
  Type: Initial release
  
• Version 1.1: 2018-08-15
  Changes: Data collection, Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary