3LDX | pdb_00003ldx

Discovery and Clinical Evaluation of RWJ-671818, a Thrombin Inhibitor with an Oxyguanidine P1 Motif

PDB DOI: https://doi.org/10.2210/pdb3LDX/pdb

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

Deposited: 2010-01-13 Released: 2011-08-10
Deposition Author(s): Spurlino, J.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.224 (Depositor), 0.218 (DCC)
R-Value Work:
0.175 (Depositor), 0.167 (DCC)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery and Clinical Evaluation of RWJ-671818, a Thrombin Inhibitor with an Oxyguanidine P1 Motif

Spurlino, J.C.

To be published.

Macromolecule Content

Total Structure Weight: 35.71 kDa
Atom Count: 2,402
Modelled Residue Count: 286
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 variant-1	C [auth I]	11	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
NLI Query on NLI 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]	N-[2-(carbamimidamidooxy)ethyl]-2-{3-[(2,2-difluoro-2-phenylethyl)amino]-6-methyl-2-oxopyrazin-1(2H)-yl}acetamide C₁₈ H₂₃ F₂ N₇ O₃ IDCKXHIGLKQWMM-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.224 (Depositor), 0.218 (DCC)
R-Value Work: 0.175 (Depositor), 0.167 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.099	α = 90
b = 72.008	β = 101.06
c = 73.412	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-08-10

Deposition Author(s):

Spurlino, J.C.

Revision History (Full details and data files)

Version 1.0: 2011-08-10
Type: Initial release
Version 1.1: 2017-07-19
Changes: Advisory, Structure summary
Version 1.2: 2024-11-27
Changes: Advisory, Data collection, Database references, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

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Discovery and Clinical Evaluation of RWJ-671818, a Thrombin Inhibitor with an Oxyguanidine P1 Motif

Discovery and Clinical Evaluation of RWJ-671818, a Thrombin Inhibitor with an Oxyguanidine P1 Motif

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

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