5IXY | pdb_00005ixy

Lactate Dehydrogenase in complex with hydroxylactam inhibitor compound 31: (2~{S})-5-(2-chlorophenyl)sulfanyl-2-(4-morpholin-4-ylphenyl)-4-oxidanyl-2-thiophen-3-yl-1,3-dihydropyridin-6-one

PDB DOI: https://doi.org/10.2210/pdb5IXY/pdb

Classification: OXIREDUCTASE/OXIREDUCTASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-03-23 Released: 2016-09-14
Deposition Author(s): Chen, Z., Eigenbrot, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.279 (Depositor), 0.285 (DCC)
R-Value Work:
0.236 (Depositor), 0.244 (DCC)
R-Value Observed:
0.237 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Cell Active Hydroxylactam Inhibitors of Human Lactate Dehydrogenase with Oral Bioavailability in Mice.

Purkey, H.E., Robarge, K., Chen, J., Chen, Z., Corson, L.B., Ding, C.Z., DiPasquale, A.G., Dragovich, P.S., Eigenbrot, C., Evangelista, M., Fauber, B.P., Gao, Z., Ge, H., Hitz, A., Ho, Q., Labadie, S.S., Lai, K.W., Liu, W., Liu, Y., Li, C., Ma, S., Malek, S., O'Brien, T., Pang, J., Peterson, D., Salphati, L., Sideris, S., Ultsch, M., Wei, B., Yen, I., Yue, Q., Zhang, H., Zhou, A.

(2016) ACS Med Chem Lett 7: 896-901

PubMed: 27774125 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.6b00190
Primary Citation Related Structures:
5IXS, 5IXY

PubMed Abstract:
A series of trisubstituted hydroxylactams was identified as potent enzymatic and cellular inhibitors of human lactate dehydrogenase A. Utilizing structure-based design and physical property optimization, multiple inhibitors were discovered with <10 μM lactate IC ₅₀ in a MiaPaca2 cell line. Optimization of the series led to 29 , a potent cell active molecule (MiaPaca2 IC ₅₀ = 0.67 μM) that also possessed good exposure when dosed orally to mice.

Organizational Affiliation

Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States.

Macromolecule Content

Total Structure Weight: 151.74 kDa
Atom Count: 10,593
Modeled Residue Count: 1,321
Deposited Residue Count: 1,324
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase A chain	A, B, C, D	331	Homo sapiens	Mutation(s): 0 Gene Names: LDHA, PIG19 EC: 1.1.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for P00338 (Homo sapiens) Explore P00338 Go to UniProtKB: P00338
PHAROS: P00338 GTEx: ENSG00000134333
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00338
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D]	E [auth A], I [auth B], N [auth C], R [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain R [auth D]
GN2 Query on GN2 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain S [auth D] SDF format, chain Q [auth C] SDF format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain S [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain S [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B]	H [auth A], M [auth B], Q [auth C], S [auth D]	(2~{S})-5-(2-chlorophenyl)sulfanyl-2-(4-morpholin-4-ylphenyl)-4-oxidanyl-2-thiophen-3-yl-1,3-dihydropyridin-6-one C₂₅ H₂₃ Cl N₂ O₃ S₂ SUFXXEIVBZJOAP-VWLOTQADSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain S [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain S [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B]	F [auth A] G [auth A] J [auth B] K [auth B] L [auth B] F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], O [auth C], P [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
GN2	BindingDB: 5IXY	IC50: 55 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.279 (Depositor), 0.285 (DCC)
R-Value Work: 0.236 (Depositor), 0.244 (DCC)
R-Value Observed: 0.237 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.452	α = 90
b = 80.696	β = 97.9
c = 102.236	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-09-14

Deposition Author(s):

Chen, Z.

Eigenbrot, C.

Revision History (Full details and data files)

Version 1.0: 2016-09-14
Type: Initial release
Version 1.1: 2016-11-09
Changes: Database references
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

5IXY | pdb_00005ixy

Lactate Dehydrogenase in complex with hydroxylactam inhibitor compound 31: (2~{S})-5-(2-chlorophenyl)sulfanyl-2-(4-morpholin-4-ylphenyl)-4-oxidanyl-2-thiophen-3-yl-1,3-dihydropyridin-6-one

Literature

Cell Active Hydroxylactam Inhibitors of Human Lactate Dehydrogenase with Oral Bioavailability in Mice.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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