Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

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

Macromolecule Content

• Total Structure Weight: 35.51 kDa 
• Atom Count: 2602 
• Modelled Residue Count: 286 
• Deposited Residue Count: 299 
• Unique protein chains: 4

1RIW

Thrombin in complex with natural product inhibitor Oscillarin

• PDB DOI: 10.2210/pdb1RIW/pdb

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


• Deposited: 2003-11-18 Released: 2004-11-09 
• Deposition Author(s): Hanessian, S., Tremblay, M., Petersen, J.F.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.232 
• R-Value Work: 0.213 

Literature

The N-acyloxyiminium ion aza-Prins route to octahydroindoles: total synthesis and structural confirmation of the antithrombotic marine natural product oscillarin

Hanessian, S., Tremblay, M., Petersen, J.F.W.

(2004) J Am Chem Soc 126: 6064-6071

• PubMed: 15137772 
• DOI: 10.1021/ja030669g
• Primary Citation of Related Structures:  
  1RIW


• PubMed Abstract: 
  

The first enantiocontrolled total synthesis of the marine natural product oscillarin is described. The proposed structure and absolute configuration of oscillarin is thus confirmed, and a previously assigned structure of a subunit was shown to be incorrect. The X-ray structure of an oscillarin-thrombin complex was resolved at 2.0 A resolution, which validated its potent inhibitory activity against the enzyme with an IC(50) = 28 nM. Methodology was developed for the synthesis of enantiopure octahydroindole-2-carboxylic acids with usable functionality at C-6. The method consists of the halocarbocyclization of N-acyloxyiminium ions containing an olefinic tether in the presence of tin tetrachloride or tin tetrabromide. This N-acyloxyiminium ion aza-Prins carbocyclization proved to be general for the construction of octahydroindole and perhydroquinoline 2-carboxylic acids. Mechanistic rationales are based on an antiperiplanar attack of the terminal alkene on the iminium ion, leading to an incipient secondary carbocation which is trapped by halide via an equatorial attack. X-ray crystal structures of products corroborate the expected stereochemistry.

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Organizational Affiliation: 

Department of Chemistry, Université de Montréal, C.P. 6128, Station Centre-ville, Montréal, P.Q., H3C 3J7 Canada. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
thrombin light chain	A	36	Homo sapiens	Mutation(s): 0  Gene Names: F2 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
thrombin heavy chain, B	B	147	Homo sapiens	Mutation(s): 0  Gene Names: F2 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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
thrombin heavy chain, C	C	105	Homo sapiens	Mutation(s): 0  Gene Names: F2 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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Hirudin IIB	D	11	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P28504 (Hirudo medicinalis) Explore P28504  Go to UniProtKB:  P28504

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OSC	H [auth C]	(2R,3AS,6R,7AS)-N-(2-{1-[AMINO(IMINO)METHYL]-2,5-DIHYDRO-1H-PYRROL-3-YL}ETHYL)-6-HYDROXY-1-{N-[(2S)-2-HYDROXY-3-PHENYLPROPANOYL]PHENYLALANYL}OCTAHYDRO-1H-INDOLE-2-CARBOXAMIDE C34 H44 N6 O5 YNAKQOCSOOKXJP-VCNFNBSBSA-N
NAG	E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA	F [auth C], G [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
OSC	PDBBind:  1RIW	IC50: 28 (nM) from 1 assay(s)
	BindingDB:  1RIW	IC50: 28 (nM) from 1 assay(s)
	Binding MOAD:  1RIW	IC50: 28 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.232 
• R-Value Work: 0.213 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.055	α = 90
b = 72.366	β = 100.19
c = 70.83	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
MOSFLM	data reduction
CCP4	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-11-18 
• Released Date: 2004-11-09 
Deposition Author(s): Hanessian, S., Tremblay, M., Petersen, J.F.W.

Revision History  

• Version 1.0: 2004-11-09
  Type: Initial release
  
• Version 1.1: 2008-04-29
  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: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary