6Q0D: Ldha
Crystal structure of ldha in complex with compound NCGC00384414-01 at 2.05 a resolution. Determined by X-ray diffraction at 2.05 Å resolution. Released 23 Sept 2020.
- Method
- X-ray diffraction
- Resolution
- 2.05 Å
- Organism
- Homo sapiens
- Chains
- 6
- Atoms
- 16,383
- Mol. weight
- 229.26 kDa
- Ligands
- PO4, P8M, NAI
- Released
- 23 Sept 2020
Explore 6Q0D in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6Q0D contains 101 α-helices and 86 β-strands across 6 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: 15 helices, 13 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 | 54-65 | 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 | 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 | 185-190 | 6 | 2 |
| β-strand | 196-205 | 10 | 2 |
| β-strand | 208-209 | 2 | 2 |
| 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: 17 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-7 | 5 | |
| β-strand | 8-10 | 3 | 3 |
| α-helix | 14-16 | 3 | |
| β-strand | 21-25 | 5 | 4 |
| α-helix | 29-40 | 12 | |
| β-strand | 46-50 | 5 | 4 |
| α-helix | 54-66 | 13 | |
| 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 | 185-190 | 6 | 4 |
| β-strand | 196-205 | 10 | 4 |
| β-strand | 208-209 | 2 | 4 |
| α-helix | 210-213 | 4 | |
| α-helix | 227-244 | 18 | |
| 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, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-7 | 5 | |
| β-strand | 8-10 | 3 | 4 |
| β-strand | 21-25 | 5 | 3 |
| α-helix | 29-40 | 12 | |
| β-strand | 46-50 | 5 | 3 |
| α-helix | 54-66 | 13 | |
| 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 | 184-185 | 2 | 5 |
| β-strand | 188-189 | 2 | 6 |
| β-strand | 190 | 1 | 3 |
| 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 | 3 |
| β-strand | 287-295 | 9 | 3 |
| β-strand | 298-303 | 6 | 3 |
| α-helix | 309-326 | 18 | |
Chain D: 18 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-7 | 5 | |
| β-strand | 8-10 | 3 | 2 |
| α-helix | 14-16 | 3 | |
| 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 | |
| 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 | 184-185 | 2 | 7 |
| β-strand | 188-190 | 3 | 1 |
| β-strand | 196-198 | 3 | 1 |
| 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 | 249-264 | 16 | |
| β-strand | 268-275 | 8 | 1 |
| β-strand | 287-295 | 9 | 1 |
| β-strand | 298-303 | 6 | 1 |
| α-helix | 309-328 | 20 | |
Chain E: 16 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-7 | 5 | |
| β-strand | 8-10 | 3 | 8 |
| β-strand | 21-25 | 5 | 9 |
| α-helix | 29-40 | 12 | |
| β-strand | 46-50 | 5 | 9 |
| α-helix | 54-66 | 13 | |
| α-helix | 68-70 | 3 | |
| β-strand | 75-78 | 4 | 9 |
| α-helix | 82-85 | 4 | |
| β-strand | 90-93 | 4 | 9 |
| α-helix | 99-100 | 2 | |
| α-helix | 105-126 | 22 | |
| α-helix | 130 | 1 | |
| β-strand | 131-134 | 4 | 9 |
| α-helix | 139-150 | 12 | |
| α-helix | 154-156 | 3 | |
| β-strand | 157-159 | 3 | 9 |
| α-helix | 163-177 | 15 | |
| α-helix | 181-183 | 3 | |
| β-strand | 184-189 | 6 | 10 |
| β-strand | 190 | 1 | 9 |
| β-strand | 197-205 | 9 | 10 |
| β-strand | 208-209 | 2 | 10 |
| α-helix | 210-213 | 4 | |
| α-helix | 227-244 | 18 | |
| α-helix | 249-263 | 15 | |
| β-strand | 268-275 | 8 | 9 |
| β-strand | 287-295 | 9 | 9 |
| β-strand | 298-303 | 6 | 9 |
| α-helix | 309-326 | 18 | |
Chain F: 18 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-7 | 5 | |
| β-strand | 8-10 | 3 | 9 |
| 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 | 75-78 | 4 | 8 |
| α-helix | 82-85 | 4 | |
| β-strand | 90-93 | 4 | 8 |
| α-helix | 97-100 | 4 | |
| α-helix | 105-126 | 22 | |
| 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 | 11 |
| β-strand | 188-190 | 3 | 8 |
| α-helix | 193-195 | 3 | |
| β-strand | 196-198 | 3 | 8 |
| 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 | 8 |
| β-strand | 287-295 | 9 | 8 |
| β-strand | 298-303 | 6 | 8 |
| α-helix | 309-326 | 18 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| L-lactate dehydrogenase A chain | A, B, C, D, E, F | protein | 332 | Homo sapiens | P00338 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F), FASTA
>6Q0D_1 L-lactate dehydrogenase A chain (chains A, B, C, D, E, F)
MATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKG
EMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFI
IPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGV
HPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYE
VIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGI
SDLVKVTLTSEEEARLKKSADTLWGIQKELQF
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| PO4 | Phosphate ion | O4 P | 6 |
| P8M | 2-{3-[3-(cyclopentylethynyl)-4-fluorophenyl]-5-(cyclopropylmethyl)-4-[(3-fluoro… | C31 H28 F2 N4 O4 S2 | 6 |
| NAI | 1,4-dihydronicotinamide adenine dinucleotide | C21 H29 N7 O14 P2 | 6 |
Water and common crystallization additives (GOL) are not listed.
Primary citation
Pyrazole-Based Lactate Dehydrogenase Inhibitors with Optimized Cell Activity and Pharmacokinetic Properties. Rai, G., Urban, D.J., Mott, B.T. et al. J Med Chem (2020) 63:10984-11011. DOI 10.1021/acs.jmedchem.0c00916 · 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…
Browse structure collections
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