6FTM | pdb_00006ftm

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-048

PDB DOI: https://doi.org/10.2210/pdb6FTM/pdb

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

Deposited: 2018-02-22 Released: 2019-03-20
Deposition Author(s): Singh, A.K., Brown, D.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.198 (Depositor), 0.210 (DCC)
R-Value Work:
0.157 (Depositor), 0.170 (DCC)
R-Value Observed:
0.159 (Depositor)

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-048

de Heuvel, E., Singh, A.K., Brown, D.G.

To be published.

Macromolecule Content

Total Structure Weight: 84.27 kDa
Atom Count: 5,796
Modeled Residue Count: 666
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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
E6Z (Subject of Investigation/LOI) Query on E6Z Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain PA [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain PA [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain PA [auth B]	BA [auth A], PA [auth B]	3-{5-[(4aR,8aS)-3-cycloheptyl-4-oxo-3,4,4a,5,8,8a-hexahydrophthalazin-1-yl]-2-methoxyphenyl}prop-2-ynamide C₂₅ H₂₉ N₃ O₃ YALZXZYFCQHHIY-LEWJYISDSA-N		Interactions Focus chain BA [auth A] Focus chain PA [auth B] Interactions & Density Focus chain BA [auth A] Focus chain PA [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain EA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain EA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain EA [auth B]	D [auth A], EA [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain EA [auth B] Interactions & Density Focus chain D [auth A] Focus chain EA [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain N [auth A] SDF format, chain LA [auth B] SDF format, chain L [auth A] SDF format, chain KA [auth B] SDF format, chain K [auth A] SDF format, chain HA [auth B] SDF format, chain H [auth A] SDF format, chain GA [auth B] SDF format, chain FA [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain N [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain N [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain E [auth A]	E [auth A] F [auth A] FA [auth B] G [auth A] GA [auth B] E [auth A], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], N [auth A], O [auth A], P [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]
GAI Query on GAI Download Ideal Coordinates CCD File SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A]	MA [auth B] NA [auth B] Q [auth A] R [auth A] S [auth A] MA [auth B], NA [auth B], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A]	GUANIDINE C H₅ N₃ ZRALSGWEFCBTJO-UHFFFAOYSA-N		Interactions Focus chain MA [auth B] Focus chain NA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain MA [auth B] Focus chain NA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain CA [auth A] SDF format, chain OA [auth B] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	AA [auth A], CA [auth A], OA [auth B], Y [auth A], Z [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain CA [auth A] Focus chain OA [auth B] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain CA [auth A] Focus chain OA [auth B] Focus chain Y [auth A] Focus chain Z [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain DA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain DA [auth B] mmCIF format, chain C [auth A] mmCIF format, chain DA [auth B]	C [auth A], DA [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain DA [auth B] Interactions & Density Focus chain C [auth A] Focus chain DA [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
E6Z	BindingDB: 6FTM	Ki: 631 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.198 (Depositor), 0.210 (DCC)
R-Value Work: 0.157 (Depositor), 0.170 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.052	α = 90
b = 114.73	β = 109.43
c = 63.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-03-20

Deposition Author(s):

Singh, A.K.

Brown, D.G.

Revision History (Full details and data files)

Version 1.0: 2019-03-20
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description