4M49: Lactate Dehydrogenase A

Lactate Dehydrogenase A in complex with a substituted pyrazine inhibitor compound 18. Determined by X-ray diffraction at 2.05 Å resolution. Released 4 Sept 2013.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,248
Mol. weight: 151.28 kDa
Ligands: LAC, 22Y, NAI
Released: 4 Sept 2013

Explore 4M49 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4M49 contains 69 α-helices and 64 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: 18 helices, 16 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	98-100	3
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	184-185	2	3
β-strand	188-189	2	4
β-strand	190	1	2
β-strand	197-198	2	4
α-helix	200-202	3
β-strand	204-205	2	3
β-strand	208-209	2	3
α-helix	210-213	4
α-helix	227-244	18
α-helix	249-263	15
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: 18 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	8-10	3	5
β-strand	21-25	5	6
α-helix	29-40	12
β-strand	46-50	5	6
α-helix	54-66	13
α-helix	68-70	3
β-strand	75-78	4	6
α-helix	82-85	4
β-strand	90-93	4	6
α-helix	99-100	2
α-helix	105-108	4
α-helix	109-126	18
α-helix	130	1
β-strand	131-134	4	6
α-helix	139-150	12
α-helix	154-156	3
β-strand	157-159	3	6
α-helix	163-177	15
α-helix	181-183	3
β-strand	184-185	2	7
β-strand	188-189	2	8
β-strand	190	1	6
β-strand	197-198	2	8
α-helix	200-202	3
β-strand	204-205	2	7
β-strand	208-209	2	7
α-helix	210-213	4
α-helix	227-244	18
α-helix	249-263	15
β-strand	268-275	8	6
β-strand	287-295	9	6
β-strand	298-303	6	6
α-helix	309-326	18

Chain C: 17 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	8-10	3	6
β-strand	21-25	5	5
α-helix	29-40	12
β-strand	46-50	5	5
α-helix	54-65	12
α-helix	68-70	3
β-strand	75-79	5	5
α-helix	82-85	4
β-strand	90-93	4	5
α-helix	105-126	22
α-helix	130	1
β-strand	131-134	4	5
α-helix	139-150	12
α-helix	154-156	3
β-strand	157-159	3	5
α-helix	163-177	15
α-helix	181-183	3
β-strand	184-185	2	9
β-strand	188-189	2	10
β-strand	190	1	5
β-strand	197-198	2	10
α-helix	200-202	3
β-strand	204-205	2	9
β-strand	208-209	2	9
α-helix	210-213	4
α-helix	227-234	8
α-helix	236-244	9
α-helix	249-263	15
β-strand	268-275	8	5
β-strand	287-295	9	5
β-strand	298-303	6	5
α-helix	309-326	18

Chain D: 16 helices, 16 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	105-126	22
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	184-185	2	11
β-strand	188-189	2	12
β-strand	190	1	1
β-strand	197-198	2	12
α-helix	200-202	3
β-strand	204-205	2	11
β-strand	208-209	2	11
α-helix	210-213	4
α-helix	227-244	18
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

>4M49_1 L-lactate dehydrogenase A chain (chains A, B, C, D)
ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGE
MMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFII
PNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVH
PLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEV
IKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGIS
DLVKVTLTSEEEARLKKSADTLWGIQKELQF

Ligands and cofactors

ID	Name	Formula	Copies
LAC	Lactic acid	C3 H6 O3	1
22Y	3-(5-amino-6-{[(1R)-1-phenylethyl]amino}pyrazin-2-yl)-4-chlorobenzoic acid	C19 H17 Cl N4 O2	3
NAI	1,4-dihydronicotinamide adenine dinucleotide	C21 H29 N7 O14 P2	4

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

Primary citation

Identification of 2-amino-5-aryl-pyrazines as inhibitors of human lactate dehydrogenase. Fauber, B.P., Dragovich, P.S., Chen, J. et al. Bioorg Med Chem Lett (2013) 23:5533-5539. DOI 10.1016/j.bmcl.2013.08.060 · PubMed

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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