6T89

Thrombin in complex with (S)-N-(tert-butyl)-4-(3-(3-carbamimidoylphenyl)-2-((2',4'-dimethoxy-[1,1'-biphenyl])-3-sulfonamido)propanoyl)piperazine-1-carboxamide (MI-498)

• PDB DOI: https://doi.org/10.2210/pdb6T89/pdb

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


• Deposited: 2019-10-24 Released: 2020-11-18 
• Deposition Author(s): Ngaha, S.A., Sandner, A., Huber, S., Heine, A., Steinmetzer, T., Pilgram, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.215 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Literature

Improving the selectivity of 3-amidinophenylalanine-derived matriptase inhibitors

Pilgram, O., Keils, A., Benary, G.E., Muller, J., Merkl, S., Ngaha, S., Huber, S., Chevillard, F., Harbig, A., Magdolen, V., Heine, A., Bottcher-Friebertshauser, E., Steinmetzer, T.

(2022) Eur J Med Chem : 114437

• DOI: https://doi.org/10.1016/j.ejmech.2022.114437

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.37 kDa 
• Atom Count: 2,525 
• Modelled Residue Count: 289 
• Deposited Residue Count: 307 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	A [auth L]	36	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	B [auth H]	259	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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hirudin variant-2	C [auth I]	12	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P09945 (Hirudo medicinalis) Explore P09945  Go to UniProtKB:  P09945

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MUQ	D [auth H]	4-[(2~{S})-3-(3-carbamimidoylphenyl)-2-[[3-(4-methoxy-2-oxidanyl-phenyl)phenyl]sulfonylamino]propanoyl]-~{N}-methyl-piperazine-1-carboxamide C29 H34 N6 O6 S YIECQHSXDOLVBZ-VWLOTQADSA-N
NAG	E [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
DMS	H	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NA	F [auth H], G [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS	C [auth I]	L-PEPTIDE LINKING	C9 H11 N O6 S		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.215 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.914	α = 90
b = 71.829	β = 100.95
c = 72.158	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Ngaha, S.A., Sandner, A., Huber, S., Heine, A., Steinmetzer, T., Pilgram, O.

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2022-06-01
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Refinement description