4RLS | pdb_00004rls

Lactate Dehydrogenase in complex with inhibitor compound 47

PDB DOI: https://doi.org/10.2210/pdb4RLS/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-10-17 Released: 2014-11-12
Deposition Author(s): Eigenbrot, C., Ultsch, M.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.233 (Depositor), 0.233 (DCC)
R-Value Work:
0.192 (Depositor), 0.197 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Identification of 3,6-disubstituted dihydropyrones as inhibitors of human lactate dehydrogenase.

Fauber, B.P., Dragovich, P.S., Chen, J., Corson, L.B., Ding, C.Z., Eigenbrot, C., Labadie, S., Malek, S., Peterson, D., Purkey, H.E., Robarge, K., Sideris, S., Ultsch, M., Wei, B., Yen, I., Yue, Q., Zhou, A.

(2014) Bioorg Med Chem Lett 24: 5683-5687

PubMed: 25467161 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2014.10.067
Primary Citation Related Structures:
4RLS

PubMed Abstract:
A series of 3,6-disubstituted dihydropyrones were identified as inhibitors of human lactate dehydrogenase (LDH)-A. Structure activity relationships were explored and a series of 6,6-spiro analogs led to improvements in LDHA potency (IC50 <350 nM). An X-ray crystal structure of an improved compound bound to human LDHA was obtained and it illustrated additional opportunities to enhance the potency of these compounds, resulting in the identification of 51 (IC50=30 nM).

Organizational Affiliation

Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.

Macromolecule Content

Total Structure Weight: 149.81 kDa
Atom Count: 11,196
Modeled Residue Count: 1,310
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI Query on NAI Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain L [auth D] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain L [auth D] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain L [auth D] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], L [auth D]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D]
49C Query on 49C Download:Ideal Coordinates CCD File SDF format, chain M [auth D] MOL2 format, chain M [auth D] mmCIF format, chain M [auth D]	M [auth D]	(1R)-5'-[(2-chlorophenyl)sulfanyl]-4'-hydroxy-2,3-dihydrospiro[indene-1,2'-pyran]-6'(3'H)-one C₁₉ H₁₅ Cl O₃ S RBPDUTMGGGWCRQ-LJQANCHMSA-N		Interactions Focus chain M [auth D] Interactions & Density Focus chain M [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain F [auth A]	F [auth A], J [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain J [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth C]
2OP Query on 2OP Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B]	H [auth B], K [auth C]	(2S)-2-HYDROXYPROPANOIC ACID C₃ H₆ O₃ JVTAAEKCZFNVCJ-REOHCLBHSA-N		Interactions Focus chain H [auth B] Focus chain K [auth C] Interactions & Density Focus chain H [auth B] Focus chain K [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.233 (Depositor), 0.233 (DCC)
R-Value Work: 0.192 (Depositor), 0.197 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.234	α = 90
b = 81.758	β = 98.28
c = 104.563	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-11-12

Deposition Author(s):

Eigenbrot, C.

Ultsch, M.H.

Revision History (Full details and data files)

Version 1.0: 2014-11-12
Type: Initial release
Version 1.1: 2014-12-24
Changes: Database references
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations