6QGP

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-0769

PDB DOI: https://doi.org/10.2210/pdb6QGP/pdb

Classification: HYDROLASE
Organism(s): Trypanosoma brucei
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-01-12 Released: 2020-02-05
Deposition Author(s): Singh, A.K., Blaazer, A.R., Zara, L., de Esch, I.J.P., Leurs, R., Brown, D.G.
Funding Organization(s): European Union

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.225
R-Value Work: 0.179
R-Value Observed: 0.181

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 structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-0769

Singh, A.K., Brown, D.G.

To be published.

Macromolecule Content

Total Structure Weight: 82.89 kDa
Atom Count: 5,790
Modelled Residue Count: 665
Deposited Residue Count: 720
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphodiesterase	A, B	360	Trypanosoma brucei	Mutation(s): 0 Gene Names: PDEB1 EC: 3.1.4
UniProt
Find proteins for Q8WQX9 (Trypanosoma brucei) Explore Q8WQX9 Go to UniProtKB: Q8WQX9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8WQX9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
J2E (Subject of Investigation/LOI) Query on J2E Download Ideal Coordinates CCD File SDF format, chain U [auth B] MOL2 format, chain U [auth B]	U [auth B]	1-cycloheptyl-3-[3-(cyclopentyloxy)-4-methoxyphenyl]-4,4-dimethyl-4,5-dihydro-1H-pyrazol-5-one C₂₄ H₃₄ N₂ O₃ MDEBQDIFTFRECC-UHFFFAOYSA-N		Interactions Focus chain U [auth B] Interactions & Density Focus chain U [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B]	T [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B]	J [auth A] K [auth A] L [auth A] P [auth B] Q [auth B] J [auth A], K [auth A], L [auth A], P [auth B], Q [auth B], R [auth B], S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain M [auth B]	C [auth A], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain M [auth B]
GAI Query on GAI Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain H [auth A]	H [auth A], I [auth A], O [auth B]	GUANIDINE C H₅ N₃ ZRALSGWEFCBTJO-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	E [auth A], F [auth A], G [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain N [auth B]	D [auth A], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain N [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
J2E	BindingDB: 6QGP	IC50: 410 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.225
R-Value Work: 0.179
R-Value Observed: 0.181
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.621	α = 90
b = 115.344	β = 108.32
c = 68.585	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-02-05

Deposition Author(s):

Funding Organization	Location	Grant Number
European Union		602666

Revision History (Full details and data files)

Version 1.0: 2020-02-05
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description