2BDY

thrombin in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2BDY/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, Hirudo medicinalis
• Mutation(s): No 


• Deposited: 2005-10-21 Released: 2006-10-24 
• Deposition Author(s): Xue, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.225 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 

Literature

Phenolic P2/P3 core motif as thrombin inhibitors--design, synthesis, and X-ray co-crystal structure.

Hanessian, S., Therrien, E., van Otterlo, W.A., Bayrakdarian, M., Nilsson, I., Xue, Y.

(2006) Bioorg Med Chem Lett 16: 1032-1036

• PubMed: 16290930 
• DOI: https://doi.org/10.1016/j.bmcl.2005.10.082
• Primary Citation of Related Structures:  
  2BDY


• PubMed Abstract: 
  

  Prototypical thrombin inhibitors were synthesized based on a trisubstituted phenol as a core motif. A naphthylsulfonamide analogue showed excellent antithrombin activity. An X-ray co-crystal structure showed the expected interactions.

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Organizational Affiliation: 

Department of Chemistry, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, PQ, Canada H3C 3J7. [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: 35.17 kDa 
• Atom Count: 2,719 
• Modelled Residue Count: 286 
• Deposited Residue Count: 299 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin	A	289	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
Hirudin IIIB'	B	10	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P01050 (Hirudo medicinalis) Explore P01050  Go to UniProtKB:  P01050

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNB	D [auth A]	N-(4-CARBAMIMIDOYL-BENZYL)-2-[2-HYDROXY-6-METHYL-3-(NAPHTHALENE-1-SULFONYLAMINO)-PHENYL]-ACETAMIDE C27 H26 N4 O4 S KWJVADNYZMUTJY-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS	B	L-PEPTIDE LINKING	C9 H11 N O6 S		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
UNB	PDBBind:  2BDY	IC50: 17 (nM) from 1 assay(s)
	BindingDB:  2BDY	IC50: 17 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.225 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.918	α = 90
b = 71.649	β = 99.56
c = 71.234	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-24 
Deposition Author(s): Xue, Y.

Revision History  

• Version 1.0: 2006-10-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2013-03-13
  Changes: Other
• Version 1.5: 2017-10-18
  Changes: Refinement description