1A5G | pdb_00001a5g

HUMAN THROMBIN COMPLEXED WITH NOVEL SYNTHETIC PEPTIDE MIMETIC INHIBITOR AND HIRUGEN

PDB DOI: https://doi.org/10.2210/pdb1A5G/pdb

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

Deposited: 1998-02-16 Released: 1998-05-27
Deposition Author(s): St Charles, R., Tulinsky, A., Kahn, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Work:
0.158 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Bound structures of novel P3-P1' beta-strand mimetic inhibitors of thrombin.

St Charles, R., Matthews, J.H., Zhang, E., Tulinsky, A.

(1999) J Med Chem 42: 1376-1383

PubMed: 10212123 Search on PubMed
DOI: https://doi.org/10.1021/jm980052n
Primary Citation Related Structures:
1A46, 1A5G, 1A61, 1B5G

PubMed Abstract:
The X-ray crystal structures of four beta-strand-templated active site inhibitors of thrombin containing P1' groups have been determined and refined at about 2.1-A resolution to crystallographic R-values between 0.148 and 0.164. Two of the inhibitors have an alpha-ketoamide functionality at the scissile bond; the other two have a nonhydrolyzable electrophilic group at the P1' position. The binding of lysine is compared with that of arginine at the S1 specificity site, while that of D,L-phenylalanine enantiomorphs is compared in the S3 region of thrombin. Four different P1' moieties bind at the S1' subsite in three different ways. The binding constants vary between 2.0 microM and 70 pM. The bound structures are used to intercorrelate the various binding constants and also lead to insightful inferences concerning binding at the S1' site of thrombin.

Organizational Affiliation

Department of Chemistry, Michigan State University, East Lansing, Michigan 48823, USA.

Macromolecule Content

Total Structure Weight: 36.04 kDa
Atom Count: 2,513
Modeled Residue Count: 287
Deposited Residue Count: 307
Unique protein chains: 3

Macromolecules

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| 3D Structure

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00734
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00734
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HIRUGEN	C [auth I]	12	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P09945 (Hirudo medicinalis) Explore P09945 Go to UniProtKB: P09945
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09945
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
00L Query on 00L Download:Ideal Coordinates CCD File SDF format, chain F [auth H] MOL2 format, chain F [auth H] mmCIF format, chain F [auth H]	F [auth H]	(1S,7S)-7-amino-7-benzyl-N-[(1S)-4-carbamimidamido-1-{(1S)-1-hydroxy-2-oxo-2-[(2-phenylethyl)amino]ethyl}butyl]-8-oxohexahydro-1H-pyrazolo[1,2-a]pyridazine-1-carboxamide C₃₀ H₄₂ N₈ O₄ BCHJOEWNJFXZEK-DNHJLFCISA-N		Interactions Focus chain F [auth H]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth H] SDF format, chain D [auth H] MOL2 format, chain E [auth H] MOL2 format, chain D [auth H] mmCIF format, chain E [auth H] mmCIF format, chain D [auth H]	D [auth H], E [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Focus chain E [auth H]

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

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000618 (00L) Query on PRD_000618	F [auth H]	MOL-126	Peptide-like / Thrombin inhibitor		Interactions Focus chain F [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Work: 0.158 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.81	α = 90
b = 72.25	β = 100.8
c = 72.79	γ = 90

Software Package:

Software Name	Purpose
R-AXIS	data collection
R-AXIS	data reduction
PROFFT	refinement
R-AXIS	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 1998-05-27

Deposition Author(s):

St Charles, R.

Tulinsky, A.

Kahn, M.

Revision History (Full details and data files)

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
Version 1.4: 2024-06-05
Changes: Data collection, Database references, Derived calculations, Other
Version 1.5: 2024-11-13
Changes: Structure summary