6T9U

Bovine Trypsine in complex with the synthetic inhibitor (S)-3'-(N-(1-(4-(3-(tert-butyl)ureido)piperidin-1-yl)-3-(3-carbamimidoylphenyl)-1-oxopropan-2-yl)sulfamoyl)-[1,1'-biphenyl]-3-carboximidamide (MI-490)

PDB DOI: https://doi.org/10.2210/pdb6T9U/pdb

Classification: HYDROLASE
Organism(s): Bos taurus
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.07 Å
R-Value Free: 0.151
R-Value Work: 0.135
R-Value Observed: 0.136

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 26.76 kDa
Atom Count: 2,039
Modelled Residue Count: 223
Deposited Residue Count: 246
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cationic Trypsin	A	246	Bos taurus	Mutation(s): 0 EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus) Explore P00760 Go to UniProtKB: P00760
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00760
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MZE (Subject of Investigation/LOI) Query on MZE Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	1-~{tert}-butyl-3-[1-[(2~{S})-3-(3-carbamimidoylphenyl)-2-[[3-(3-carbamimidoylphenyl)phenyl]sulfonylamino]propanoyl]piperidin-4-yl]urea C₃₃ H₄₂ N₈ O₄ S JFMRSUSVFPNDAU-NDEPHWFRSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
TFA Query on TFA Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	trifluoroacetic acid C₂ H F₃ O₂ DTQVDTLACAAQTR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain D [auth A]	B [auth A], D [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain D [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.07 Å
R-Value Free: 0.151
R-Value Work: 0.135
R-Value Observed: 0.136
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.631	α = 90
b = 55.631	β = 90
c = 109.764	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-11-18

Deposition Author(s):

Revision History (Full details and data files)

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

Prepare Data

Validate Data

Deposit Data

Help and Resources

6T9U

Bovine Trypsine in complex with the synthetic inhibitor (S)-3'-(N-(1-(4-(3-(tert-butyl)ureido)piperidin-1-yl)-3-(3-carbamimidoylphenyl)-1-oxopropan-2-yl)sulfamoyl)-[1,1'-biphenyl]-3-carboximidamide (MI-490)

Improving the selectivity of 3-amidinophenylalanine-derived matriptase inhibitors

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)