1YPJ

Thrombin Inhibitor Complex

PDB DOI: https://doi.org/10.2210/pdb1YPJ/pdb

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

Deposited: 2005-01-31 Released: 2006-01-17
Deposition Author(s): Fokkens, J., Obst-Sander, U., Heine, A., Diederich, F., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.239
R-Value Work: 0.195
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.7 of the entry. See complete history.

Literature

A simple protocol to estimate differences in protein binding affinity for enantiomers without prior resolution of racemates

Fokkens, J., Klebe, G.

(2006) Angew Chem Int Ed Engl 45: 985-989

PubMed: 16374786 Search on PubMed
DOI: https://doi.org/10.1002/anie.200502302
Primary Citation of Related Structures:
1Y3V, 1Y3W, 1Y3X, 1Y3Y, 1YP9, 1YPE, 1YPG, 1YPJ, 1YPK

Organizational Affiliation

Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Germany.

Macromolecule Content

Total Structure Weight: 34.59 kDa
Atom Count: 2,534
Modelled Residue Count: 288
Deposited Residue Count: 294
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]	27	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 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]	257	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 Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hirudin	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 Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UIB Query on UIB 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]	(1R,3AS,4R,8AS,8BR)-4-{5-(PHENYL[1,3]DIOXOL-5-YLMETHYL)-4-ETHYL-2,3,3-TRIMETHYL-6-OXO-OCTAHYDRO-PYRROLO[3,4-C]PYRROL-1-YL}-BENZAMIDINE C₂₆ H₃₂ N₄ O₃ HQVPEQYGMUJQHM-MSYGRNIXSA-N		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [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

Binding Affinity Annotations
ID	Source	Binding Affinity
UIB	PDBBind: 1YPJ	Ki: 95 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.239
R-Value Work: 0.195
R-Value Observed: 0.195
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.521	α = 90
b = 71.809	β = 99.87
c = 71.308	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-01-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-01-17
Type: Initial release
Version 1.1: 2008-04-30
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: 2013-11-13
Changes: Other
Version 1.6: 2017-10-11
Changes: Refinement description
Version 1.7: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary