9H5N | pdb_00009h5n

Crystal structure of Thrombin in complex with a Chlorothiophene-based inhibitor, CP3, discovered by a novel rapid nanoscale library screening.

• PDB DOI: https://doi.org/10.2210/pdb9H5N/pdb

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


• Deposited: 2024-10-22 Released: 2025-11-05 
• Deposition Author(s): Chinellato, M., Zsolt, B., Angelini, A., Heinis, C., Cendron, L.
• Funding Organization(s): Italian Ministry of Education

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.284 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.263 (Depositor), 0.263 (DCC) 
• R-Value Observed: 
  0.264 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 72.53 kDa 
• Atom Count: 4,740 
• Modeled Residue Count: 573 
• Deposited Residue Count: 616 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	A, C	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	B, D	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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P00734-1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ISR (Subject of Investigation/LOI)	E [auth B], H [auth D]	~{N}-[(3~{S})-4-[3-(2-azanyl-2-oxidanylidene-ethyl)sulfanylpropylamino]-4-oxidanylidene-3-(2-phenylethanoylamino)butyl]-5-chloranyl-thiophene-2-carboxamide C22 H27 Cl N4 O4 S2 LWUPTHGARXCPBD-INIZCTEOSA-N
NAG	F [auth B], G [auth B], I [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.284 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.263 (Depositor), 0.263 (DCC) 
• R-Value Observed: 0.264 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.931	α = 90
b = 98.26	β = 90
c = 145.661	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Chinellato, M., Zsolt, B., Angelini, A., Heinis, C., Cendron, L.

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Funding Organization	Location	Grant Number
Italian Ministry of Education	Italy	--

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release