1OYT

COMPLEX OF RECOMBINANT HUMAN THROMBIN WITH A DESIGNED FLUORINATED INHIBITOR

PDB DOI: https://doi.org/10.2210/pdb1OYT/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens, Hirudo medicinalis
Expression System: Cricetulus griseus
Mutation(s): Yes

Deposited: 2003-04-07 Released: 2003-06-24
Deposition Author(s): Banner, D.W., Olsen, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.205
R-Value Work: 0.179

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

A Fluorine Scan of Thrombin Inhibitors to Map the Fluorophilicity/Fluorophobicity of an Enzyme Active Site: Evidence for CF...C=O Interactions.

Olsen, J.A., Banner, D.W., Seiler, P., Obst-Sander, U., D'Arcy, A., Stihle, M., Mueller, K., Diederich, F.

(2003) Angew Chem Int Ed Engl 42: 2507-2511

PubMed: 12800172 Search on PubMed
DOI: https://doi.org/10.1002/anie.200351268
Primary Citation of Related Structures:
1OYT

Organizational Affiliation

Laboratorium für Organische Chemie, ETH-Hönggerberg, HCI, 8093 Zürich, Switzerland.

Macromolecule Content

Total Structure Weight: 35.74 kDa
Atom Count: 2,728
Modelled Residue Count: 283
Deposited Residue Count: 306
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00734
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% 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
Hirudin IIB	C [auth I]	11	Hirudo medicinalis	Mutation(s): 1
UniProt
Find proteins for P28506 (Hirudo medicinalis) Explore P28506 Go to UniProtKB: P28506
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28506
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FSN Query on FSN 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]	(3ASR,4RS,8ASR,8BRS)-4-(2-(4-FLUOROBENZYL)-1,3-DIOXODEACAHYDROPYRROLO[3,4-A] PYRROLIZIN-4-YL)BENZAMIDINE C₂₃ H₂₄ F N₄ O₂ GJYCQHGTXMVIBG-MUGJNUQGSA-O		Interactions Focus chain F [auth H] Interactions & Density Focus chain F [auth H]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth H] MOL2 format, chain E [auth H] mmCIF format, chain E [auth H]	E [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Interactions & Density Focus chain E [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth H] MOL2 format, chain D [auth H] mmCIF format, chain D [auth H]	D [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]

Binding Affinity Annotations
ID	Source	Binding Affinity
FSN	PDBBind: 1OYT	Ki: 57 (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_000481 Query on PRD_000481	C [auth I]	N-terminal Asp des-amino Hirudin-3A'	Oligopeptide / Anticoagulant, Antithrombotic		Interactions Focus chain C [auth I] Interactions & Density Focus chain C [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.205
R-Value Work: 0.179
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.693	α = 90
b = 71.479	β = 100.53
c = 72.802	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
MAR345	data collection
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2003-06-24

Deposition Author(s):

Banner, D.W.

Olsen, J.A.

Revision History (Full details and data files)

Version 1.0: 2003-06-24
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: 2024-04-03
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description