Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 35.35 kDa 
• Atom Count: 2551 
• Residue Count: 298 
• Unique protein chains: 3

4AYV

Human thrombin - inhibitor complex

• DOI: 10.2210/pdb4AYV/pdb

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


• Deposited: 2012-06-22 Released: 2012-08-15 
• Deposition Author(s): Banner, D.W., D'Arcy, A., Winkler, F.K., Hilpert, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.192 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 

Literature

Design and Synthesis of Potent and Highly Selective Thrombin Inhibitors.

Hilpert, K., Ackermann, J., Banner, D.W., Gast, A., Gubernator, K., Hadvary, P., Labler, L., Muller, K., Schmid, G., Tschopp, T.B.

(1994) J Med Chem 37: 3889

• PubMed: 7966150 
• DOI: 10.1021/jm00049a008
• Primary Citation of Related Structures:  
  4AX9, 4AYV, 4AYY, 4AZ2


• PubMed Abstract: 
  

Thrombin, a serine protease, plays a central role in the initiation and propagation of thrombotic events. An extensive search for new thrombin inhibitors was performed, using an unconventional approach. Screening of small basic molecules for binding in the recognition pocket of thrombin led to the discovery of (aminoiminomethyl)piperidine (amidinopiperidine) as a weak, but intrinsically selective, thrombin inhibitor. Elaboration of this molecule provided compounds which inhibit thrombin with Ki's in the range of 20-50 nM and with selectivities of 1000-4000 against trypsin. These inhibitor compounds show a new and unexpected binding mode to thrombin. Modification of the central building block and then of one of the hydrophobic substituents led to the discovery of a new family of thrombin inhibitors which has reverted to the former binding mode to thrombin. This last class of compounds shows inhibitory activities in the picomolar range, low toxicity, and a short plasma half life which favors its use for an intravenous application. From this series of thrombin inhibitors, 19f(Ro 46-6240) was selected for clinical development as an antithrombotic agent for intravenous administration.

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Organizational Affiliation: 

Pharma Division, F. Hoffmann-La Roche Ltd., Basel, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN LIGHT CHAIN	A	30	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN HEAVY CHAIN	B	257	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HIRUDIN-3A'	D	11	Hirudo medicinalis	Mutation(s): 0
Find proteins for P28508 (Hirudo medicinalis) Explore P28508  Go to UniProtKB:  P28508

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9MQ	B	{Benzyl-[(S)-3-[((S)-1-carbamimidoyl-piperidin-3-ylmethyl)-carbamoyl]-2-(naphthalene-2-sulfonylamino)-propionyl]-amino}-acetic acid C30 H36 N6 O6 S ZWJYDBRLGHLMKT-NVQXNPDNSA-N
NAG	B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA	B	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
9MQ	Ki :  0.6800000071525574   nM  PDBBind
9MQ	Ki:  0.6800000071525574   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.192 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.8	α = 90
b = 90.8	β = 90
c = 132.5	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-06-22 
• Released Date: 2012-08-15 
Deposition Author(s): Banner, D.W., D'Arcy, A., Winkler, F.K., Hilpert, K.

Revision History 

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2013-08-07
  Changes: Other
• Version 1.2: 2017-06-28
  Changes: Data collection
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary