8Q4B

Endothiapepsin in complex with ligand (3R,5R)-3-(2-((methyl(prop-2-yn-1-yl)amino)methyl)thiazol-4-yl)-5-(3-(2-nitrophenyl)-1,2,4-oxadiazol-5-yl)pyrrolidin-3-ol (CBWS-SE-163.1)

PDB DOI: https://doi.org/10.2210/pdb8Q4B/pdb

Classification: HYDROLASE
Organism(s): Cryphonectria parasitica
Mutation(s): No

Deposited: 2023-08-05 Released: 2024-08-14
Deposition Author(s): Mueller, J.M., Eckelt, S., Klebe, G., Glinca, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free: 0.207
R-Value Work: 0.192
R-Value Observed: 0.193

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structures of Endothiapepsin with ligands derived from merged fragment hits

Mueller, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 34.94 kDa
Atom Count: 2,703
Modelled Residue Count: 330
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endothiapepsin	A	330	Cryphonectria parasitica	Mutation(s): 0 EC: 3.4.23.22
UniProt
Find proteins for P11838 (Cryphonectria parasitica) Explore P11838 Go to UniProtKB: P11838
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11838
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JCI (Subject of Investigation/LOI) Query on JCI 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]	(3~{R},5~{R})-3-[2-[[ethynyl(methyl)amino]methyl]-1,3-thiazol-4-yl]-5-[3-(2-nitrophenyl)-1,2,4-oxadiazol-5-yl]pyrrolidin-3-ol C₁₉ H₁₈ N₆ O₄ S MEVOALTZQOOEHC-BFUOFWGJSA-N		Interactions Focus chain B [auth A]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain G [auth A] mmCIF format, chain C [auth A] mmCIF format, chain G [auth A]	C [auth A], G [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain C [auth A] Focus chain G [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	F [auth A], H [auth A], I [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A]