Target candidate with partial support; inspect missing evidence before prioritizing.
4 signalsStrengths
Risks / watch
How to read this page
PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.
AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.
ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.
pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.
FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.
Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.
PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.
ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.
ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.
LigQ / LigQ_2: an internal TPW pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.
Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.
DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.
Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.
EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.
KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.
Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.
Overview
Basic information about this protein and its source genome.
- Accession
- PA0927
- Gene
- ldhA PA0927
- Status
- annotated
- Amino acids
- 329
- 3D evidence
- Experimental + AlphaFold DB model
Target profile
Computed evidence for target prioritization.
- Human off-target
- hit
- Human identity (%)
- 42.623
- Human E-value
- 2e-20
- Gut microbiome off-target
- hit
- Essential (DEG)
- Y
- Localization
- Cytoplasmic
Selected pocket evidence
The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.
Sequence
Primary amino-acid sequence viewer.
MRILFFSSQAYDSESFQASNHRHGFELHFQQAHLQADTAVLAQGFEVVCAFVNDDLSRPVLERLAAGGTRLVALRSAGYNHVDLAAAEALGLPVVHVPAYSPHAVAEHAVGLILTLNRRLHRAYNRTREGDFSLHGLTGFDLHGKRVGVIGTGQIGETFARIMAGFGCELLAYDPYPNPRIQALGGRYLALDALLAESDIVSLHCPLTADTRHLIDAQRLATMKPGAMLINTGRGALVNAAALIEALKSGQLGYLGLDVYEEEADIFFEDRSDQPLQDDVLARLLSFPNVVVTAHQAFLTREALAAIADTTLDNIAAWQDGTPRNRVRA
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Gene Ontology (GO)
3- GO:0008720 Catalysis of the reaction: (R)-lactate + NAD+ = H+ + NADH + pyruvate.
- GO:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
- GO:0016616 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 102 | 297 | FunFam | G3DSA:3.40.50.720:FF:000050 | D-lactate dehydrogenase |
| 1 | 323 | PANTHER | PTHR43026 | 2-HYDROXYACID DEHYDROGENASE HOMOLOG 1-RELATED |
| 1 | 323 | CDD | cd12183 | LDH_like_2 |
| 102 | 297 | Gene3D | G3DSA:3.40.50.720 | - |
| 194 | 216 | ProSitePatterns | PS00670 | D-isomer specific 2-hydroxyacid dehydrogenases signature 2. |
| 194 | 216 | InterPro | IPR029753 | D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site |
| 3 | 327 | Pfam | PF00389 | D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain |
| 3 | 327 | InterPro | IPR006139 | D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain |
| 223 | 239 | ProSitePatterns | PS00671 | D-isomer specific 2-hydroxyacid dehydrogenases signature 3. |
| 223 | 239 | InterPro | IPR029753 | D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site |
| 6 | 318 | Gene3D | G3DSA:3.40.50.720 | - |
| 2 | 134 | SUPERFAMILY | SSF52283 | Formate/glycerate dehydrogenase catalytic domain-like |
| 147 | 174 | ProSitePatterns | PS00065 | D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. |
| 147 | 174 | InterPro | IPR029752 | D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 |
| 110 | 297 | Pfam | PF02826 | D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain |
| 110 | 297 | InterPro | IPR006140 | D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain |
| 102 | 298 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains |
| 102 | 298 | InterPro | IPR036291 | NAD(P)-binding domain superfamily |
3D Structure
Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.
Loading 3D structure...
Structural evidence
2 + 1Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer
Pockets (FPOCKET)
Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).
| FPOCKET | Sticks | Spheres | Surfaces | Druggability | Labels | Zoom | Positions |
|---|---|---|---|---|---|---|---|
| 1 | 0.702 |
Pockets (P2RANK)
Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).
| P2RANK | Sticks | Spheres | Surfaces | Score | Probability | Labels | Zoom | Positions |
|---|---|---|---|---|---|---|---|---|
| 1 | 15.59 | 0.757 | ||||||
| 2 | 4.31 | 0.179 | ||||||
| 3 | 2.73 | 0.082 | ||||||
| 4 | 1.72 | 0.03 |
Pockets (FPOCKET)
Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).
| FPOCKET | Sticks | Spheres | Surfaces | Druggability | Labels | Zoom | Positions |
|---|---|---|---|---|---|---|---|
| 1 | 0.727 | ||||||
| 3 | 0.299 |
Ligand evidence
Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.
Structural ligand evidence is available for this target.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.
No PDB structure with a co-crystallized ligand found for this exact protein.
Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.
| Ligand | Source crystal | UniProt (homolog) | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| AZI RCSB PDB | A9SQZ2 | 42.0 Da LogP 0.87 TPSA 58.7 | ✓ Ro5 | Alert |
[N-]=[N+]=[N-]
|
|
| GLV RCSB PDB | Q8U3Y2 | 74.0 Da LogP -0.73 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
C(=O)C(=O)O
|
|
| HPV RCSB PDB | P9WNX3 | 184.0 Da LogP -1.25 TPSA 121.1 | ✓ Ro5 | ✓ Clean |
C(C(=O)C(=O)O)OP(=O)(O)O
|
|
| LAC RCSB PDB | O66939 | 90.1 Da LogP -0.55 TPSA 57.5 | ✓ Ro5 | ✓ Clean |
C[C@H](C(=O)O)O
|
|
| MLI RCSB PDB | F8AEA4 | 102.0 Da LogP -3.12 TPSA 80.3 | ✓ Ro5 | ✓ Clean |
C(C(=O)[O-])C(=O)[O-]
|
|
| PPI RCSB PDB | O66939 | 74.1 Da LogP 0.48 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
CCC(=O)O
|
|
| TLA RCSB PDB | P9WNX3 | 150.1 Da LogP -2.12 TPSA 115.1 | ✓ Ro5 | ✓ Clean |
[C@@H]([C@H](C(=O)O)O)(C(=O)O)O
|
Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL bioactivity data found for this exact protein.
Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL hits found through similar proteins.
Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).
| Ligand | Tanimoto | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|
| ZINC12359024 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)C(=O)O
|
| ZINC13533920 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O
|
| ZINC1532740 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)C(=O)O
|
| ZINC1549593 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O
|
| ZINC2013424 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)C(=O)O
|
| ZINC3581021 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O
|
| ZINC3860635 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)C(=O)O
|
| ZINC5783661 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(=O)O
|
| ZINC6072527 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O
|
| ZINC1560405156 ZINC | 0.588 | 208.1 Da LogP -1.79 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)/C(O)=C(\O)[C@H](O)[C@H](O)C(=O)O
|
| ZINC1560405157 ZINC | 0.588 | 208.1 Da LogP -1.79 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)/C(O)=C(/O)[C@H](O)[C@H](O)C(=O)O
|
| ZINC1529331 ZINC | 0.500 | 206.1 Da LogP -2.21 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
O=C(O)C(=O)[C@H](C(=O)O)[C@@H](O)C(=O)O
|
| ZINC1529332 ZINC | 0.500 | 206.1 Da LogP -2.21 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
O=C(O)C(=O)[C@H](C(=O)O)[C@H](O)C(=O)O
|
| ZINC1529333 ZINC | 0.500 | 206.1 Da LogP -2.21 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
O=C(O)C(=O)[C@@H](C(=O)O)[C@@H](O)C(=O)O
|
| ZINC1529334 ZINC | 0.500 | 206.1 Da LogP -2.21 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
O=C(O)C(=O)[C@@H](C(=O)O)[C@H](O)C(=O)O
|
PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.