9BK2: Lactate dehydrogenase

Crystal structure of Lactate dehydrogenase in complex with 4-((4-(1-methyl-1H-imidazole-2-carbonyl)phenyl)amino)-4-oxo-2-(4-(trifluoromethyl)phenyl)butanoic acid (S-enantiomer, monoclinic P form). Determined by X-ray diffraction at 1.85 Å resolution. Released 10 Jul 2024.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,713
Mol. weight: 158.26 kDa
Ligands: MLI, A1AQ0
Released: 10 Jul 2024

Explore 9BK2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BK2 contains 72 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
β-strand	21-25	5	2
α-helix	29-40	12
β-strand	46-50	5	2
α-helix	54-66	13
α-helix	68-70	3
β-strand	75-79	5	2
α-helix	82-85	4
β-strand	90-93	4	2
α-helix	105-108	4
α-helix	109-126	18
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	185	1	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
α-helix	279-281	3
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	2
β-strand	21-25	5	1
α-helix	29-40	12
β-strand	46-50	5	1
α-helix	54-66	13
α-helix	68-70	3
β-strand	75-79	5	1
α-helix	82-85	4
β-strand	90-93	4	1
α-helix	105-108	4
α-helix	109-126	18
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	185	1	5
β-strand	188-189	2	6
β-strand	190	1	1
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	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

Chain C: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	8-10	3	7
α-helix	15-18	4
β-strand	21-25	5	8
α-helix	29-40	12
β-strand	46-50	5	8
α-helix	54-66	13
α-helix	68-70	3
β-strand	76-79	4	8
α-helix	82-85	4
β-strand	90-93	4	8
α-helix	99-100	2
α-helix	105-108	4
α-helix	109-126	18
α-helix	130	1
β-strand	131-134	4	8
α-helix	139-150	12
α-helix	154-156	3
β-strand	157-159	3	8
α-helix	163-177	15
α-helix	181-183	3
β-strand	185	1	9
β-strand	188-189	2	10
β-strand	190	1	8
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	227-244	18
α-helix	249-263	15
β-strand	268-275	8	8
β-strand	287-295	9	8
β-strand	298-303	6	8
α-helix	309-326	18

Chain D: 18 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	8-10	3	8
α-helix	15-18	4
β-strand	21-25	5	7
α-helix	29-40	12
β-strand	46-50	5	7
α-helix	54-66	13
α-helix	68-70	3
β-strand	75-79	5	7
α-helix	82-85	4
β-strand	90-93	4	7
α-helix	105-108	4
α-helix	109-126	18
α-helix	130	1
β-strand	131-134	4	7
α-helix	139-150	12
α-helix	154-156	3
β-strand	157-159	3	7
α-helix	163-177	15
α-helix	181-183	3
β-strand	185	1	11
β-strand	188-189	2	12
β-strand	190	1	7
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	7
β-strand	287-295	9	7
β-strand	298-303	6	7
α-helix	309-326	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
L-lactate dehydrogenase A chain	A, B, C, D	protein	352	Homo sapiens	P00338 (AlphaFold model)

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

>9BK2_1 L-lactate dehydrogenase A chain (chains A, B, C, D)
MHHHHHHSTSVDLGTENLYFQATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISIL
MKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQ
QEGESRLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIG
SGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGT
DKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGL
YGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF

Ligands and cofactors

ID	Name	Formula	Copies
MLI	Malonate ion	C3 H2 O4	10
A1AQ0	(2S)-4-[4-(1-methyl-1H-imidazole-2-carbonyl)anilino]-4-oxo-2-[4-(trifluoromethy…	C22 H18 F3 N3 O4	1

Water and common crystallization additives (DMS) are not listed.

Primary citation

Synthesis and biological characterization of an orally bioavailable lactate dehydrogenase-A inhibitor against pancreatic cancer. Sharma, H., Mondal, S., Urquiza, U. et al. Eur J Med Chem (2024) 275:116598-116598. DOI 10.1016/j.ejmech.2024.116598 · 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
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…
6MVA 2.02 Å, LDHA structure in complex with inhibitor 14

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