6BB2

Lactate Dehydrogenase in complex with inhibitor (S)-5-((2-chlorophenyl)thio)-6'-(4-fluorophenoxy)-4-hydroxy-2-(thiophen-3-yl)-2,3-dihydro-[2,2'-bipyridin]-6(1H)-one

PDB DOI: https://doi.org/10.2210/pdb6BB2/pdb

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

Deposited: 2017-10-16 Released: 2018-10-24
Deposition Author(s): Ultsch, M., Eigenbrot, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free: 0.236
R-Value Work: 0.190
R-Value Observed: 0.190

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Structure-guided optimization and in vivo activities of hydroxylactone and hydroxylactam Inhibitors of Human Lactate Dehydrogenase

Wei, B., Labadie, S.S., 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., Goa, Z., Ge, H., Hitz, A., Ho, Q., 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., Yen, I., Yue, Q., Zhang, H., Zhou, A., Purkey, H.E.

To be published.

Macromolecule Content

Total Structure Weight: 300.74 kDa
Atom Count: 21,396
Modelled Residue Count: 2,618
Deposited Residue Count: 2,648
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase A chain	A, B, C, D, E A, B, C, D, E, F, G, H	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00338
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 AA [auth G] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain V [auth E] SDF format, chain X [auth F] SDF format, chain CA [auth H] MOL2 format, chain AA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] MOL2 format, chain CA [auth H] mmCIF format, chain AA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain V [auth E] mmCIF format, chain X [auth F] mmCIF format, chain CA [auth H]	AA [auth G] CA [auth H] I [auth A] L [auth B] O [auth C] AA [auth G], CA [auth H], I [auth A], L [auth B], O [auth C], Q [auth D], V [auth E], X [auth F]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AA [auth G] Focus chain CA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain V [auth E] Focus chain X [auth F] Interactions & Density Focus chain AA [auth G] Focus chain CA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain V [auth E] Focus chain X [auth F]
D4J Query on D4J Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain U [auth D] SDF format, chain W [auth E] MOL2 format, chain BA [auth G] MOL2 format, chain U [auth D] MOL2 format, chain W [auth E] mmCIF format, chain BA [auth G] mmCIF format, chain U [auth D] mmCIF format, chain W [auth E]	BA [auth G], U [auth D], W [auth E]	(2S)-5-[(2-chlorophenyl)sulfanyl]-6'-(4-fluorophenoxy)-4-hydroxy-2-(thiophen-3-yl)-2,3-dihydro[2,2'-bipyridin]-6(1H)-one C₂₆ H₁₈ Cl F N₂ O₃ S₂ XFNQOQKMMIFYDK-SANMLTNESA-N		Interactions Focus chain BA [auth G] Focus chain U [auth D] Focus chain W [auth E] Interactions & Density Focus chain BA [auth G] Focus chain U [auth D] Focus chain W [auth E]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain Y [auth F] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain Y [auth F] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain Y [auth F]	J [auth A] M [auth B] R [auth D] S [auth D] T [auth D] J [auth A], M [auth B], R [auth D], S [auth D], T [auth D], Y [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Focus chain M [auth B] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain Y [auth F] Interactions & Density Focus chain J [auth A] Focus chain M [auth B] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain Y [auth F]
LAC Query on LAC Download Ideal Coordinates CCD File SDF format, chain DA [auth H] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain Z [auth F] MOL2 format, chain DA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Z [auth F] mmCIF format, chain DA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Z [auth F]	DA [auth H], K [auth A], N [auth B], P [auth C], Z [auth F]	LACTIC ACID C₃ H₆ O₃ JVTAAEKCZFNVCJ-UWTATZPHSA-N		Interactions Focus chain DA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain Z [auth F] Interactions & Density Focus chain DA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free: 0.236
R-Value Work: 0.190
R-Value Observed: 0.190
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.183	α = 90
b = 158.561	β = 90
c = 264.978	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-10-24

Deposition Author(s):

Ultsch, M.

Eigenbrot, C.

Revision History (Full details and data files)

Version 1.0: 2018-10-24
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection