5TEI | pdb_00005tei

Structure of human ALDH1A1 with inhibitor CM039

PDB DOI: https://doi.org/10.2210/pdb5TEI/pdb

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

Deposited: 2016-09-21 Released: 2017-09-27
Deposition Author(s): Morgan, C.A., Hurley, T.D.
Funding Organization(s): National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.227 (Depositor), 0.233 (DCC)
R-Value Work:
0.179 (Depositor), 0.185 (DCC)
R-Value Observed:
0.181 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of human ALDH1A1 with inhibitor CM039

Hurley, T.D., Morgan, C.A., Buchman, C.D.

To be published.

Macromolecule Content

Total Structure Weight: 56.31 kDa
Atom Count: 4,040
Modeled Residue Count: 493
Deposited Residue Count: 501
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinal dehydrogenase 1	A	501	Homo sapiens	Mutation(s): 1 Gene Names: ALDH1A1, ALDC, ALDH1, PUMB1 EC: 1.2.1.36 (PDB Primary Data), 1.2.1.19 (UniProt), 1.2.1.28 (UniProt), 1.2.1.3 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00352 (Homo sapiens) Explore P00352 Go to UniProtKB: P00352
PHAROS: P00352 GTEx: ENSG00000165092
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00352
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI Query on NAI Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
M39 Query on M39 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	6-{[(3-fluorophenyl)methyl]sulfanyl}-5-(2-methylphenyl)-2,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one C₁₉ H₁₅ F N₄ O S SSEVBNPAVKLWFQ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
YB Query on YB Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	YTTERBIUM (III) ION Yb AWSFICBXMUKWSK-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.227 (Depositor), 0.233 (DCC)
R-Value Work: 0.179 (Depositor), 0.185 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.818	α = 90
b = 108.818	β = 90
c = 82.954	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-09-27

Deposition Author(s):

Morgan, C.A.

Hurley, T.D.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)	United States	R01AA018123

Revision History (Full details and data files)

Version 1.0: 2017-09-27
Type: Initial release
Version 1.1: 2019-12-11
Changes: Author supporting evidence
Version 1.2: 2024-03-06
Changes: Data collection, Database references, Derived calculations