Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 35.99 kDa 
• Atom Count: 2485 
• Residue Count: 286 
• Unique protein chains: 3

1TBZ

HUMAN THROMBIN WITH ACTIVE SITE N-METHYL-D PHENYLALANYL-N-[5-(AMINOIMINOMETHYL)AMINO]-1-{{BENZOTHIAZOLYL)CARBONYL] BUTYL]-L-PROLINAMIDE TRIFLUROACETATE AND EXOSITE-HIRUGEN

• DOI: 10.2210/pdb1TBZ/pdb

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


• Deposited: 1998-02-05 Released: 1998-05-27 
• Deposition Author(s): Matthews, J.H., Krishnan, R., Costanzo, M.J., Maryanoff, B.E., Tulinsky, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Work: 0.158 

Literature

Crystal structures of thrombin with thiazole-containing inhibitors: probes of the S1' binding site.

Matthews, J.H., Krishnan, R., Costanzo, M.J., Maryanoff, B.E., Tulinsky, A.

(1996) Biophys J 71: 2830-2839

• PubMed: 8913620 
• DOI: 10.1016/S0006-3495(96)79479-1
• Primary Citation of Related Structures:  
  1TBZ, 1A4W


• PubMed Abstract: 
  

Structures of the blood clotting enzyme thrombin complexed with hirugen and two active site inhibitors, RWJ-50353 10080(N-methyl-D-phenylalanyl-N-[5-[(aminoiminomethyl)amino]-1- [[(2-benzothiazolyl)carbonyl]butyl]-L-prolinamide trifluoroacetate hydrate) and RWJ-50215 (N-[4-(aminoiminomethyl)amino-1-[2- (thiazol-2-ylcarbonylethyl)piperidin- 1-ylcarbonyl]butyl]-5-(dimethylamino)naphthalenesulfonamide trifluoroacetate hydrate), were determined by x-ray crystallography. The refinements converged at R values of 0.158 in the 7.0-2.3-A range for RWJ-50353 and 0.155 in the 7.0-1.8-A range for RWJ-50215. Interactions between the protein and the thiazole rings of the two inhibitors provide new valuable information about the S1' binding site of thrombin. The RWJ-50353 inhibitor consists of an S1'-binding benzothiazole group linked to the D-Phe-Pro-Arg chloromethyl ketone motif. Interactions with the S1-S3 sites are similar to the D-phenylalanyl-prolyl-arginyl chloromethylketone structure. In RWJ-50215, a S1'-binding 2-ketothiazole group was added to the thrombin inhibitor-like framework of dansylarginine N-(3-ethyl-1,5-pentanediyl)amide. The geometry at the S1-S3 sites here is also similar to that of the parent compound. The benzothiazole and 2-ketothiazole groups bind in a cavity surrounded by His57, Tyr60A, Trp60D, and Lys60F. This location of the S1' binding site is consistent with previous structures of thrombin complexes with hirulog-3, CVS-995, and hirutonin-2 and -6. The ring nitrogen of the RWJ-50353 benzothiazole forms a hydrogen bond with His57, and Lys60F reorients because of close contacts. The oxygen and nitrogen of the ketothiazole of RWJ-50215 hydrogen bond with the NZ atom of Lys60F.

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Related Citations: 

• The Isomorphous Structures of Prethrombin2, Hirugen-, and Ppack-Thrombin: Changes Accompanying Activation and Exosite Binding to Thrombin
  Vijayalakshmi, J., Padmanabhan, K.P., Mann, K.G., Tulinsky, A.
  (1994) Protein Sci 3: 2254

• Active Site and Exosite Binding of Alpha-Thrombin
  Tulinsky, A., Qiu, X.
  (1993) Blood Coagul Fibrinolysis 4: 305

• Structure of the Hirulog 3-Thrombin Complex and Nature of the S' Subsites of Substrates and Inhibitors
  Qiu, X., Padmanabhan, K.P., Carperos, V.E., Tulinsky, A., Kline, T., Maraganore, J.M., Fenton II, J.W.
  (1992) Biochemistry 31: 11689

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Organizational Affiliation: 

Department of Chemistry, Michigan State University, East Lansing 48824, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-THROMBIN	L	36	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
ALPHA-THROMBIN	H	259	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
HIRUGEN	I	12	Hirudo medicinalis	Mutation(s): 0
Find proteins for P09945 (Hirudo medicinalis) Explore P09945  Go to UniProtKB:  P09945

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
00Q	H	D-phenylalanyl-N-{(1S)-1-[(S)-1,3-benzothiazol-2-yl(hydroxy)methyl]-4-carbamimidamidobutyl}-L-prolinamide C27 H35 N7 O3 S FOIAKHMJUJAMDU-ANZJIFDASA-N
NA	H	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000621 (00Q)	H	RWJ-30353	Peptide-like /  Thrombin inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Work: 0.158 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.79	α = 90
b = 72.53	β = 101
c = 73.12	γ = 90

Software Package:

Software Name	Purpose
XENGEN	data collection
XENGEN	data reduction
X-PLOR	model building
X-PLOR	refinement
XENGEN	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-02-05 
• Released Date: 1998-05-27 
Deposition Author(s): Matthews, J.H., Krishnan, R., Costanzo, M.J., Maryanoff, B.E., Tulinsky, A.

Revision History 

• Version 1.0: 1998-05-27
  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