9H79 | pdb_00009h79

Crystal structure of Thrombin in complex with a Chlorothiophene-based inhibitor, CP2, discovered by a novel rapid nanoscale library screening.

PDB DOI: https://doi.org/10.2210/pdb9H79/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-10-27 Released: 2025-11-05
Deposition Author(s): Chinellato, M., Zsolt, B., Angelini, A., Heinis, C., Cendron, L.
Funding Organization(s): Italian Ministry of Education

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.266 (Depositor), 0.267 (DCC)
R-Value Work:
0.204 (Depositor), 0.205 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Small molecule ligand development by nanoscale library synthesis and functional screening of crude product

Zsolt, B., Deng, X., Zarda, A., Menoud, G., Will, E., Nielsen, A.R., Farrera-Soler, L., Chinellato, M., Cendron, L., Angelini, A., Heinis, C.

To be published.

Macromolecule Content

Total Structure Weight: 144.6 kDa
Atom Count: 9,428
Modeled Residue Count: 1,139
Deposited Residue Count: 1,232
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	A, C, E, G	49	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% 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
Prothrombin	B, D, F, 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00734
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain D Focus chain F	Go to GlyGen: P00734-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1ITQ (Subject of Investigation/LOI) Query on A1ITQ Download:Ideal Coordinates CCD File SDF format, chain Q [auth H] SDF format, chain N [auth F] SDF format, chain L [auth D] SDF format, chain I [auth B] MOL2 format, chain Q [auth H] MOL2 format, chain N [auth F] MOL2 format, chain L [auth D] MOL2 format, chain I [auth B] mmCIF format, chain Q [auth H] mmCIF format, chain N [auth F] mmCIF format, chain L [auth D] mmCIF format, chain I [auth B]	I [auth B], L [auth D], N [auth F], Q [auth H]	~{N}-[(3~{S})-4-[3-(2-azanyl-2-oxidanylidene-ethyl)sulfanylpropylamino]-3-[2-(3-chlorophenyl)ethanoylamino]-4-oxidanylidene-butyl]-5-chloranyl-thiophene-2-carboxamide C₂₂ H₂₆ Cl₂ N₄ O₄ S₂ AHAKNDPOUBPYNA-INIZCTEOSA-N		Interactions Focus chain I [auth B] Focus chain L [auth D] Focus chain N [auth F] Focus chain Q [auth H] Interactions & Density Focus chain I [auth B] Focus chain L [auth D] Focus chain N [auth F] Focus chain Q [auth H]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain M [auth D] SDF format, chain O [auth F] MOL2 format, chain J [auth B] MOL2 format, chain M [auth D] MOL2 format, chain O [auth F] mmCIF format, chain J [auth B] mmCIF format, chain M [auth D] mmCIF format, chain O [auth F]	J [auth B], M [auth D], O [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth B] Focus chain M [auth D] Focus chain O [auth F] Interactions & Density Focus chain J [auth B] Focus chain M [auth D] Focus chain O [auth F]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain R [auth H] SDF format, chain P [auth F] SDF format, chain K [auth B] MOL2 format, chain R [auth H] MOL2 format, chain P [auth F] MOL2 format, chain K [auth B] mmCIF format, chain R [auth H] mmCIF format, chain P [auth F] mmCIF format, chain K [auth B]	K [auth B], P [auth F], R [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain P [auth F] Focus chain R [auth H] Interactions & Density Focus chain K [auth B] Focus chain P [auth F] Focus chain R [auth H]