1TOM

ALPHA-THROMBIN COMPLEXED WITH HIRUGEN

• PDB DOI: https://doi.org/10.2210/pdb1TOM/pdb

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


• Deposited: 1996-12-06 Released: 1997-03-12 
• Deposition Author(s): Chen, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.172 
• R-Value Observed: 0.172 

Literature

Synthesis, evaluation, and crystallographic analysis of L-371,912: A potent and selective active-site thrombin inhibitor.

Lyle, T.A., Chen, Z.G., Appleby, S.D., Freidinger, R.M., Gardell, S.J., Lewis, S.D., Li, Y., Lyle, E.A., Lynch, J.J., Mulichak, A.M., Ng, A.S., NaylorOlsen, A.M., Sanders, W.M.

(1997) Bioorg Med Chem Lett 7: 67-72

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.87 kDa 
• Atom Count: 2,553 
• Modelled Residue Count: 286 
• Deposited Residue Count: 307 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-THROMBIN	A [auth L]	36	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
ALPHA-THROMBIN	B [auth H]	259	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HIRUGEN	C [auth I]	12	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P28507 (Hirudo medicinalis) Explore P28507  Go to UniProtKB:  P28507

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MIN	D [auth H]	METHYL-PHE-PRO-AMINO-CYCLOHEXYLGLYCINE C22 H34 N4 O2 MDSVGJAUFNXYRR-WTGUMLROSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
MIN	PDBBind:  1TOM	Ki: 5 (nM) from 1 assay(s)
	BindingDB:  1TOM	Ki: min: 4.9, max: 5 (nM) from 2 assay(s)
		IC50: 6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.172 
• R-Value Observed: 0.172 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.25	α = 90
b = 72.19	β = 101.85
c = 73.11	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-03-12 
Deposition Author(s): Chen, Z.

Revision History  

• Version 1.0: 1997-03-12
  Type: Initial release
  
• Version 1.1: 2008-03-24
  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: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.6: 2024-10-23
  Changes: Structure summary