6T9V | pdb_00006t9v

Bovine Trypsin 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/pdb6T9V/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.13 Å
R-Value Free:
0.152 (Depositor), 0.153 (DCC)
R-Value Work:
0.130 (Depositor), 0.133 (DCC)
R-Value Observed:
0.131 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.3 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: 26.77 kDa
Atom Count: 2,048
Modeled Residue Count: 223
Deposited Residue Count: 246
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00760
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MXH (Subject of Investigation/LOI) Query on MXH Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [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		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
TFA Query on TFA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	trifluoroacetic acid C₂ H F₃ O₂ DTQVDTLACAAQTR-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.13 Å
R-Value Free: 0.152 (Depositor), 0.153 (DCC)
R-Value Work: 0.130 (Depositor), 0.133 (DCC)
R-Value Observed: 0.131 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.464	α = 90
b = 55.464	β = 90
c = 109.142	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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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
Version 2.3: 2024-11-20
Changes: Structure summary