2V3H | pdb_00002v3h

Thrombin with 3-cycle no F

• PDB DOI: https://doi.org/10.2210/pdb2V3H/pdb

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


• Deposited: 2007-06-18 Released: 2008-06-24 
• Deposition Author(s): Banner, D.W., Obst, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.207 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Fluorine in Pharmaceuticals: Looking Beyond Intuition.

Mueller, K., Faeh, C., Diederich, F.

(2007) Science 317: 1881

• PubMed: 17901324 
• DOI: https://doi.org/10.1126/science.1131943
• Primary Citation Related Structures: 
  2V3H, 2V3O


• PubMed Abstract: 
  

  Fluorine substituents have become a widespread and important drug component, their introduction facilitated by the development of safe and selective fluorinating agents. Organofluorine affects nearly all physical and adsorption, distribution, metabolism, and excretion properties of a lead compound. Its inductive effects are relatively well understood, enhancing bioavailability, for example, by reducing the basicity of neighboring amines. In contrast, exploration of the specific influence of carbon-fluorine single bonds on docking interactions, whether through direct contact with the protein or through stereoelectronic effects on molecular conformation of the drug, has only recently begun. Here, we review experimental progress in this vein and add complementary analysis based on comprehensive searches in the Cambridge Structural Database and the Protein Data Bank.

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Organizational Affiliation: 
• Pharmaceuticals Division, Discovery Chemistry, F. Hoffmann-La Roche, CH-4070 Basel, Switzerland. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 34.78 kDa 
• Atom Count: 2,754 
• Modeled Residue Count: 284 
• Deposited Residue Count: 296 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN HEAVY CHAIN	A [auth H]	257	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 IIA	B [auth I]	11	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P28503 (Hirudo medicinalis) Explore P28503  Go to UniProtKB:  P28503

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN LIGHT CHAIN	C [auth L]	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
I25	D [auth H]	(2R)-({4-[AMINO(IMINO)METHYL]PHENYL}AMINO){3-[3-(DIMETHYLAMINO)-2,2-DIMETHYLPROPOXY]-5-ETHYLPHENYL}ACETIC ACID C24 H34 N4 O3 VVVFEPKRHINSIE-OAQYLSRUSA-N
CA	F [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	E [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000481	B [auth I]	N-terminal Asp des-amino Hirudin-3A'	Oligopeptide / Anticoagulant, Antithrombotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.207 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.44	α = 90
b = 71.78	β = 100.4
c = 72.41	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-24 
Deposition Author(s): Banner, D.W., Obst, U.

Revision History  

• Version 1.0: 2008-06-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2012-11-30
  Changes: Other
• Version 1.3: 2013-08-07
  Changes: Other
• Version 1.4: 2013-10-23
  Changes: Other
• Version 1.5: 2025-04-09
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary