3V94 | pdb_00003v94

TcrPDEC1 catalytic domain in complex with inhibitor wyq16

PDB DOI: https://doi.org/10.2210/pdb3V94/pdb

Classification: hydrolase/hydrolase inhibitor
Organism(s): Trypanosoma cruzi
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2011-12-23 Released: 2012-02-22
Deposition Author(s): Wang, H., Kunz, S., Chen, G., Seebeck, T., Wan, Y., Robinson, H., Martinelli, S., Ke, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.268 (Depositor), 0.268 (DCC)
R-Value Work:
0.224 (Depositor), 0.224 (DCC)
R-Value Observed:
0.224 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3V94

Ligand Structure Quality Assessment

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

Literature

TcrPDEC1 catalytic domain in complex with inhibitor wyq16

Wang, H., Kunz, S., Chen, G., Seebeck, T., Wan, Y., Robinson, H., Martinelli, S., Ke, H.

To be published.

Macromolecule Content

Total Structure Weight: 307.12 kDa
Atom Count: 21,762
Modeled Residue Count: 2,659
Deposited Residue Count: 2,760
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic nucleotide specific phosphodiesterase	A, B, C, D, E A, B, C, D, E, F, G, H	345	Trypanosoma cruzi	Mutation(s): 0 Gene Names: PDEC, TcrPDEC1 EC: 3.1.4.17 (PDB Primary Data), 3.1.4 (UniProt)
UniProt
Find proteins for Q53I60 (Trypanosoma cruzi) Explore Q53I60 Go to UniProtKB: Q53I60
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q53I60
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WYQ Query on WYQ Download:Ideal Coordinates CCD File SDF format, chain X [auth F] SDF format, chain U [auth E] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain DA [auth H] SDF format, chain AA [auth G] MOL2 format, chain X [auth F] MOL2 format, chain U [auth E] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain DA [auth H] MOL2 format, chain AA [auth G] mmCIF format, chain X [auth F] mmCIF format, chain U [auth E] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain DA [auth H] mmCIF format, chain AA [auth G]	AA [auth G] DA [auth H] I [auth A] L [auth B] O [auth C] AA [auth G], DA [auth H], I [auth A], L [auth B], O [auth C], R [auth D], U [auth E], X [auth F]	propan-2-yl {[4-ethoxy-3-(1-methyl-7-oxo-3-propyl-6,7-dihydro-1H-pyrazolo[4,3-d]pyrimidin-5-yl)phenyl]sulfonyl}carbamate C₂₁ H₂₇ N₅ O₆ S RGTRFWTZGHUUBF-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain DA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain AA [auth G] Focus chain DA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain V [auth E] SDF format, chain S [auth D] SDF format, chain P [auth C] SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain EA [auth H] SDF format, chain BA [auth G] MOL2 format, chain Y [auth F] MOL2 format, chain V [auth E] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain EA [auth H] MOL2 format, chain BA [auth G] mmCIF format, chain Y [auth F] mmCIF format, chain V [auth E] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain EA [auth H] mmCIF format, chain BA [auth G]	BA [auth G] EA [auth H] J [auth A] M [auth B] P [auth C] BA [auth G], EA [auth H], J [auth A], M [auth B], P [auth C], S [auth D], V [auth E], Y [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain EA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth G] Focus chain EA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain W [auth E] SDF format, chain T [auth D] SDF format, chain Q [auth C] SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain FA [auth H] SDF format, chain CA [auth G] MOL2 format, chain Z [auth F] MOL2 format, chain W [auth E] MOL2 format, chain T [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain FA [auth H] MOL2 format, chain CA [auth G] mmCIF format, chain Z [auth F] mmCIF format, chain W [auth E] mmCIF format, chain T [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain FA [auth H] mmCIF format, chain CA [auth G]	CA [auth G] FA [auth H] K [auth A] N [auth B] Q [auth C] CA [auth G], FA [auth H], K [auth A], N [auth B], Q [auth C], T [auth D], W [auth E], Z [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain FA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain FA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F]

Binding Affinity Annotations
ID	Source	Binding Affinity
WYQ	BindingDB: 3V94	IC50: min: 230, max: 230 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.268 (Depositor), 0.268 (DCC)
R-Value Work: 0.224 (Depositor), 0.224 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.147	α = 90
b = 131.147	β = 90
c = 394.861	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-02-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-22
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.