6BAD: Lactate Dehydrogenase

Lactate Dehydrogenase in complex with inhibitor (R)-3-((2-chlorophenyl)thio)-6-(3-((4-fluorophenyl)amino)phenyl)-4-hydroxy-6-(thiophen-3-yl)-5,6-dihydro-2H-pyran-2-one. Determined by X-ray diffraction at 2.1 Å resolution. Released 17 Oct 2018.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,527
Mol. weight: 153.31 kDa
Ligands: D0Y, NAD
Released: 17 Oct 2018

Explore 6BAD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BAD contains 67 α-helices and 55 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 17 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	8-10	3	1
α-helix	16-18	3
β-strand	21-25	5	2
α-helix	29-40	12
β-strand	46-50	5	2
α-helix	54-65	12
α-helix	68-70	3
β-strand	75-78	4	2
α-helix	82-85	4
β-strand	90-93	4	2
α-helix	97-100	4
α-helix	105-126	22
α-helix	130	1
β-strand	131-134	4	2
α-helix	139-150	12
α-helix	154-156	3
β-strand	157-159	3	2
α-helix	163-177	15
α-helix	181-183	3
β-strand	184-190	7	2
β-strand	196-205	10	2
β-strand	208-209	2	2
α-helix	210-213	4
α-helix	228-244	17
α-helix	249-264	16
β-strand	268-275	8	2
β-strand	287-295	9	2
β-strand	298-303	6	2
α-helix	309-326	18

Chain B: 17 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	8-10	3	3
β-strand	21-25	5	4
α-helix	29-40	12
β-strand	46-50	5	4
α-helix	54-65	12
α-helix	68-70	3
β-strand	75-78	4	4
α-helix	82-85	4
β-strand	90-93	4	4
α-helix	97-100	4
α-helix	105-126	22
α-helix	130	1
β-strand	131-134	4	4
α-helix	139-150	12
α-helix	154-156	3
β-strand	157-159	3	4
α-helix	163-177	15
α-helix	181-183	3
β-strand	185	1	5
β-strand	188-189	2	6
β-strand	190	1	4
β-strand	197-198	2	6
α-helix	200-202	3
β-strand	204-205	2	5
β-strand	208-209	2	5
α-helix	210-213	4
α-helix	228-244	17
α-helix	249-263	15
β-strand	268-275	8	4
β-strand	287-295	9	4
β-strand	298-303	6	4
α-helix	309-326	18

Chain C: 17 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	8-10	3	4
α-helix	15-18	4
β-strand	21-25	5	3
α-helix	29-40	12
β-strand	46-50	5	3
α-helix	54-65	12
α-helix	68-70	3
β-strand	75-78	4	3
α-helix	82-85	4
β-strand	90-93	4	3
α-helix	97-100	4
α-helix	105-126	22
α-helix	130	1
β-strand	131-134	4	3
α-helix	139-150	12
α-helix	154-156	3
β-strand	157-159	3	3
α-helix	163-177	15
α-helix	181-183	3
β-strand	184-190	7	3
β-strand	196-205	10	3
β-strand	208-209	2	3
α-helix	210-213	4
α-helix	228-244	17
α-helix	249-264	16
β-strand	268-275	8	3
β-strand	287-295	9	3
β-strand	298-303	6	3
α-helix	309-326	18

Chain D: 16 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	8-10	3	2
β-strand	21-25	5	1
α-helix	29-40	12
β-strand	46-50	5	1
α-helix	54-65	12
α-helix	68-70	3
β-strand	75-78	4	1
α-helix	82-85	4
β-strand	90-93	4	1
α-helix	97-100	4
α-helix	107-126	20
α-helix	130	1
β-strand	131-134	4	1
α-helix	139-150	12
α-helix	154-156	3
β-strand	157-159	3	1
α-helix	163-177	15
α-helix	181-183	3
β-strand	184-190	7	1
β-strand	196-205	10	1
β-strand	208-209	2	1
α-helix	210-213	4
α-helix	228-244	17
α-helix	249-263	15
β-strand	268-275	8	1
β-strand	287-295	9	1
β-strand	298-303	6	1
α-helix	309-326	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
L-lactate dehydrogenase A chain	A, B, C, D	protein	331	Homo sapiens	P00338 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6BAD_1 L-lactate dehydrogenase A chain (chains A, B, C, D)
ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGE
MMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFII
PNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVH
PLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEV
IKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGIS
DLVKVTLTSEEEARLKKSADTLWGIQKELQF

Ligands and cofactors

ID	Name	Formula	Copies
D0Y	(6R)-3-[(2-chlorophenyl)sulfanyl]-6-{3-[(4-fluorophenyl)amino]phenyl}-4-hydroxy…	C27 H19 Cl F N O3 S2	4
NAD	Nicotinamide-adenine-dinucleotide	C21 H27 N7 O14 P2	4

Water and common crystallization additives (SO4, EPE) are not listed.

Primary citation

Structure-guided optimization and in vivo activities of hydroxylactone and hydroxylactam Inhibitors of Human Lactate Dehydrogenase. Wei, B., Labadie, S.S., Robarge, K. et al. To be published.

Other PDB entries of the same protein (UniProt P00338 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5W8J 1.55 Å, Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 29
5W8K 1.6 Å, Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 29 and…
5W8H 1.8 Å, Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 11
9BK2 1.85 Å, Crystal structure of Lactate dehydrogenase in complex with…
4JNK 1.9 Å, Lactate Dehydrogenase A in complex with inhibitor compound 22
4RLS 1.91 Å, Lactate Dehydrogenase in complex with inhibitor compound 47
5W8I 1.95 Å, Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 23 and…
5W8L 1.95 Å, Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 59 and…
6BB0 1.95 Å, Lactate Dehydrogenase in complex with inhibitor (R)-3-((2-chlorophenyl)thio)-6-(3-((4-flu…
6MV8 1.95 Å, LDHA structure in complex with inhibitor 14
6Q13 2.0 Å, Crystal structure of ldha in complex with compound NCGC00420737-09 at 2.00 a resolution
4QO8 2.0 Å, Lactate Dehydrogenase A in complex with substituted 3-Hydroxy-2-mercaptocyclohex-2-enone…

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