7RAD | pdb_00007rad

Crystal Structure Analysis of ALDH1B1

PDB DOI: https://doi.org/10.2210/pdb7RAD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-07-01 Released: 2022-06-08
Deposition Author(s): Fernandez, D., Chen, J.K.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.260 (Depositor), 0.262 (DCC)
R-Value Work:
0.197 (Depositor), 0.202 (DCC)
R-Value Observed:
0.201 (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

Inhibitors targeted to aldehyde dehydrogenase

Fernandez, D.

(2022) Nat Chem Biol

Macromolecule Content

Total Structure Weight: 112.09 kDa
Atom Count: 7,915
Modeled Residue Count: 986
Deposited Residue Count: 986
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde dehydrogenase X, mitochondrial	A, B	493	Homo sapiens	Mutation(s): 2 Gene Names: ALDH1B1, ALDH5, ALDHX EC: 1.2.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P30837 (Homo sapiens) Explore P30837 Go to UniProtKB: P30837
PHAROS: P30837 GTEx: ENSG00000137124
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30837
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain C [auth A]	C [auth A], J [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
ZGJ (Subject of Investigation/LOI) Query on ZGJ Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A]	D [auth A], K [auth B]	3-(2-methoxyphenyl)-1-(4-phenylphenyl)-6,7,8,9-tetrahydro-5~{H}-imidazo[1,2-a][1,3]diazepine C₂₆ H₂₆ N₃ O HGDBKVRVNGXGJR-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] M [auth B] F [auth A], G [auth A], H [auth A], I [auth A], M [auth B], N [auth B], O [auth B], P [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A]	E [auth A], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.260 (Depositor), 0.262 (DCC)
R-Value Work: 0.197 (Depositor), 0.202 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.127	α = 90
b = 101.127	β = 90
c = 185.52	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-06-08

Deposition Author(s):

Fernandez, D.

Chen, J.K.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM127030
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM113100