4H80 | pdb_00004h80

Crystal structure of human ALDH3A1 with its isozyme selective inhibitor - N-[4-(4-methylsulfonyl-2-nitroanilino)phenyl]acetamide

PDB DOI: https://doi.org/10.2210/pdb4H80/pdb

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

Deposited: 2012-09-21 Released: 2013-12-25
Deposition Author(s): Hurley, T.D., Parajuli, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.255 (Depositor), 0.255 (DCC)
R-Value Work:
0.234 (Depositor), 0.236 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Kinetic and Structural Characterization of a Selective Inhibitor for Human ALDH3A1

Parajuli, B., Georgiadis, T., Fishel, M.L., Hurley, T.D.

To be published.

Macromolecule Content

Total Structure Weight: 420.76 kDa
Atom Count: 28,414
Modeled Residue Count: 3,570
Deposited Residue Count: 3,752
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde dehydrogenase, dimeric NADP-preferring	A, B, C, D, E A, B, C, D, E, F, G, H	469	Homo sapiens	Mutation(s): 1 Gene Names: ALDH3, ALDH3A1 EC: 1.2.1.5
UniProt & NIH Common Fund Data Resources
Find proteins for P30838 (Homo sapiens) Explore P30838 Go to UniProtKB: P30838
PHAROS: P30838 GTEx: ENSG00000108602
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30838
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
04T Query on 04T Download:Ideal Coordinates CCD File SDF format, chain P [auth H] SDF format, chain O [auth G] SDF format, chain N [auth F] SDF format, chain M [auth E] SDF format, chain L [auth D] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain P [auth H] MOL2 format, chain O [auth G] MOL2 format, chain N [auth F] MOL2 format, chain M [auth E] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain P [auth H] mmCIF format, chain O [auth G] mmCIF format, chain N [auth F] mmCIF format, chain M [auth E] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A] J [auth B] K [auth C] L [auth D] M [auth E] I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	N-(4-{[4-(methylsulfonyl)-2-nitrophenyl]amino}phenyl)acetamide C₁₅ H₁₅ N₃ O₅ S JXZXJHWSQKISBZ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H]

Binding Affinity Annotations
ID	Source	Binding Affinity
04T	BindingDB: 4H80	Ki: 4700 (nM) from 1 assay(s)
04T	BindingDB: 4H80	IC50: 1.60e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.255 (Depositor), 0.255 (DCC)
R-Value Work: 0.234 (Depositor), 0.236 (DCC)
R-Value Observed: 0.235 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.106	α = 112.38
b = 95.38	β = 91.68
c = 117.228	γ = 90.99

Software Package:

Software Name	Purpose
HKL-3000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-12-25

Deposition Author(s):

Hurley, T.D.

Parajuli, B.

Revision History (Full details and data files)

Version 1.0: 2013-12-25
Type: Initial release
Version 1.1: 2014-11-12
Changes: Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description