6T9T | pdb_00006t9t

Matriptase in complex with the synthetic inhibitor (S)-3-(3-(4-(3-(tert-butyl)ureido)piperidin-1-yl)-2-((3'-fluoro-4'-(hydroxymethyl)-[1,1'-biphenyl])-3-sulfonamido)-3-oxopropyl)benzimidamide (MI-1904)

• PDB DOI: https://doi.org/10.2210/pdb6T9T/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-10-28 Released: 2020-11-18 
• Deposition Author(s): Mueller, J.M., Merkl, S., Keils, A., Pilgram, O., Steinmetzer, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.202 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

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: Monomer - A1 

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

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 27.14 kDa 
• Atom Count: 2,159 
• Modeled Residue Count: 240 
• Deposited Residue Count: 241 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Suppressor of tumorigenicity 14 protein	A	241	Homo sapiens	Mutation(s): 1  Gene Names: ST14, PRSS14, SNC19, TADG15 EC: 3.4.21.109
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5Y6 (Homo sapiens) Explore Q9Y5Y6  Go to UniProtKB:  Q9Y5Y6
PHAROS:  Q9Y5Y6 GTEx:  ENSG00000149418

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MXH (Subject of Investigation/LOI)	C [auth A]	1-~{tert}-butyl-3-[1-[(2~{S})-3-(3-carbamimidoylphenyl)-2-[[3-[3-fluoranyl-4-(hydroxymethyl)phenyl]phenyl]sulfonylamino ]propanoyl]piperidin-4-yl]urea C33 H41 F N6 O5 S FQLCVDCDDCIBQS-LJAQVGFWSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.202 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.687	α = 90
b = 80.408	β = 95.71
c = 40.714	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Mueller, J.M., Merkl, S., Keils, A., Pilgram, O., Steinmetzer, T.

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 2.0: 2021-07-07
  Type: Coordinate replacement
  Reason: Ligand geometry
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2022-06-01
  Changes: Database references
• Version 2.2: 2024-01-24
  Changes: Data collection, Refinement description
• Version 2.3: 2024-11-13
  Changes: Structure summary