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1AFE|pdb_00001afe
HUMAN ALPHA-THROMBIN INHIBITION BY CBZ-PRO-AZALYS-ONP
- PDB DOI: https://doi.org/10.2210/pdb1AFE/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Homo sapiens,Hirudo medicinalis
- Mutation(s): No
- Deposited: 1997-03-06 Released: 1997-12-03
- Deposition Author(s): De Simone, G.,Balliano, G.,Milla, P.,Gallina, C.,Giordano, C.,Tarricone, C.,Rizzi, M.,Bolognesi, M.,Ascenzi, P.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Work: 0.170 (DCC)
Starting Model:experimental
View more details
wwPDB Validation 3D Report Full Report
Download MendeleyHuman alpha-thrombin inhibition by the highly selective compounds N-ethoxycarbonyl-D-Phe-Pro-alpha-azaLys p-nitrophenyl ester and N-carbobenzoxy-Pro-alpha-azaLys p-nitrophenyl ester: a kinetic, thermodynamic and X-ray crystallographic study.
De Simone, G., Balliano, G., Milla, P., Gallina, C., Giordano, C., Tarricone, C., Rizzi, M., Bolognesi, M., Ascenzi, P.(1997) J Mol Biology 269: 558-569
- PubMed: 9217260 Search on PubMed
- DOI: https://doi.org/10.1006/jmbi.1997.1037
- Primary Citation of Related Structures:
1AE8,1AFE - PubMed Abstract:
Kinetics, thermodynamics and structural aspects of human alpha-thrombin (thrombin) inhibition by newly synthesized low molecular weight derivatives of alpha-azalysine have been investigated. The thrombin catalyzed hydrolysis of N-ethoxycarbonyl-D-Phe-Pro-alpha-azaLys p-nitrophenyl ester (Eoc-D-Phe-Pro-azaLys-ONp) and N-carbobenzoxy-Pro-alpha-azaLys p-nitrophenyl ester (Cbz-Pro-azaLys-ONp) was investigated at pH 6.2 and 21.0 degrees C, and analyzed in parallel with that of N-alpha-(N,N-dimethylcarbamoyl)-alpha-azalysine p-nitrophenyl ester (Dmc-azaLys-ONp). Decarboxylation following the enzymatic hydrolysis of these p-nitrophenyl esters gave the corresponding 1-peptidyl-2(4-aminobutyl) hydrazines (peptidyl-Abh) showing properties of thrombin competitive inhibitors. Therefore, thermodynamics for the reversible binding of D-Phe-Pro-Abh, Cbz-Pro-Abh and Dmc-Abh to thrombin was examined. These results are consistent with the minimum four-step catalytic mechanism for product inhibition of serine proteinases. Eoc-D-Phe-Pro-azaLys-ONp and Eoc-D-Phe-Pro-Abh display a sub-micromolar affinity for thrombin together with a high selectivity versus homologous plasmatic and pancreatic serine proteinases acting on cationic substrates. The three-dimensional structures of the reversible non-covalent thrombin:Eoc-D-Phe-Pro-Abh and thrombin:Cbz-Pro-Abh complexes have been determined by X-ray crystallography at 2.0 A resolution (R-factor = 0.169 and 0.179, respectively), and analyzed in parallel with that of the thrombin:Dmc-azaLys acyl-enzyme adduct. Both Eoc-D-Phe-Pro-Abh and Cbz-Pro-Abh competitive inhibitors are accommodated in the thrombin active center, spanning the region between the aryl binding site and the S1 primary specificity subsite.
- Department of Chemistry, University of Napoli, Italy.
Organizational Affiliation:
Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (ALZ)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Hetero 3-mer - A1B1C1
Find Similar Assemblies
Biological assembly 1 assigned by authors.
Macromolecule Content
- Total Structure Weight: 35.8 kDa
- Atom Count: 2,623
- Modeled Residue Count: 299
- Deposited Residue Count: 305
- Unique protein chains: 3
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| ALPHA-THROMBIN (SMALL SUBUNIT) | 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 Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00734 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| ALPHA-THROMBIN (LARGE SUBUNIT) | 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 Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00734 | ||||
Glycosylation | |||||
| Glycosylation Sites: 1 | Go to GlyGen: P00734-1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| HIRUGEN | C [auth I] | 10 | Hirudo medicinalis | Mutation(s): 0 |  |
UniProt | |||||
Find proteins for P01050 (Hirudo medicinalis) Explore P01050 Go to UniProtKB: P01050 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P01050 | ||||
Sequence AnnotationsExpand | |||||
| |||||
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ALZ Query on ALZ Download Ideal Coordinates CCD File | E [auth H] | 2-[N'-(4-AMINO-BUTYL)-HYDRAZINOCARBONYL]-PYRROLIDINE-1-CARBOXYLIC ACID BENZYL ESTER C17 H26 N4 O3 MOCIXHUQBOUBAK-HNNXBMFYSA-N |  | ||
| NAG Query on NAG Download Ideal Coordinates CCD File | D [auth H] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| TYS Query on TYS | C [auth I] | L-PEPTIDE LINKING | C9 H11 N O6 S |  | TYR |
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Work: 0.170 (DCC)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 71.13 | α = 90 |
| b = 72.61 | β = 99.66 |
| c = 72.65 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MOSFLM | data reduction |
| ROTAVATA-AGROVATA | data reduction |
| CCP4 | model building |
| TNT | refinement |
| CCP4 | data scaling |
| ROTAVATA | data scaling |
| CCP4 | phasing |
Deposition Data
- Released Date: 1997-12-03 Deposition Author(s): De Simone, G.,Balliano, G.,Milla, P.,Gallina, C.,Giordano, C.,Tarricone, C.,Rizzi, M.,Bolognesi, M.,Ascenzi, P.
Revision History (Full details and data files)
- Version 1.0: 1997-12-03
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: 2012-04-11
Changes: Non-polymer description - Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Refinement description, Structure summary - Version 1.5: 2023-08-02
Changes: Advisory, Database references, Refinement description, Structure summary - Version 1.6: 2024-10-23
Changes: Data collection, Structure summary
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