1O0D

Human Thrombin complexed with a d-Phe-Pro-Arg-type Inhibitor and a C-terminal Hirudin derived exo-site inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1O0D/pdb

• Classification: BLOOD CLOTTING/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-02-21 Released: 2003-10-14 
• Deposition Author(s): Lange, U.E., Bauke, D., Hornberger, W., Mack, H., Seitz, W., Hoeffken, H.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.252 
• R-Value Work: 0.199 

Literature

D-Phe-Pro-Arg type thrombin inhibitors: unexpected selectivity by modification of the P1 moiety

Lange, U.E., Bauke, D., Hornberger, W., Mack, H., Seitz, W., Hoeffken, H.W.

(2003) Bioorg Med Chem Lett 13: 2029-2033

• PubMed: 12781189 
• DOI: https://doi.org/10.1016/s0960-894x(03)00347-0
• Primary Citation of Related Structures:  
  1NZQ, 1O0D


• PubMed Abstract: 
  

  Synthesis of thrombin inhibitors and their binding mode to thrombin is described. Modification of the P1 moiety leads to an increased selectivity versus trypsin. The observed selectivity is discussed in view of their thrombin-inhibitor complex X-ray structures.

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Organizational Affiliation: 

BASF AG, D-67056, Ludwigshafen, Germany. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B2C1D1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.85 kDa 
• Atom Count: 2,607 
• Modelled Residue Count: 295 
• Deposited Residue Count: 306 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	A [auth L]	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 [auth H]	259	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
Decapeptide Hirudin Analogue	C [auth D]	11	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
163	D [auth H]	(2-{2-[(5-CARBAMIMIDOYL-1-METHYL-1H-PYRROL-2-YLMETHYL)-CARBAMOYL]-PYRROL-1-YL}- 1-CYCLOHEXYLMETHYL-2-OXO-ETHYLAMINO)-ACETIC ACID C23 H32 N6 O4 AXMHAIYMRMPDQD-QGZVFWFLSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALC	C [auth D]	L-PEPTIDE LINKING	C9 H17 N O2		ALA
HYP	C [auth D]	L-PEPTIDE LINKING	C5 H9 N O3		PRO
SMF	C [auth D]	L-PEPTIDE LINKING	C10 H13 N O5 S		PHE

Binding Affinity Annotations
ID	Source	Binding Affinity
163	PDBBind:  1O0D	IC50: 6.2 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000480	C [auth D]	HIRUDIN ANALOGUE	Oligopeptide / Anticoagulant, Antithrombotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.252 
• R-Value Work: 0.199 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.88	α = 90
b = 71.96	β = 101.06
c = 73.52	γ = 90

Software Package:

Software Name	Purpose
SMART	data collection
X-GEN	data reduction
CNS	refinement
SMART	data reduction
X-GEN	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-10-14 
Deposition Author(s): Lange, U.E., Bauke, D., Hornberger, W., Mack, H., Seitz, W., Hoeffken, H.W.

Revision History  

• Version 1.0: 2003-10-14
  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: 2016-05-25
  Changes: Source and taxonomy
• Version 1.5: 2017-10-11
  Changes: Advisory, Refinement description
• Version 1.6: 2018-04-04
  Changes: Data collection