Protein target profile

KP13_02981

Malate dehydrogenase

Genome: KpKP13 Gene: mdh AHE42438.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GWA1
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Length 312
Pocket druggability 0.863
Direct ligand evidence 0 54 total records
Functional annotation 1 EC 9 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Independent pocket support: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 0.86, P2Rank 0.66). Use the 3D pocket comparison to verify whether they identify the same site. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.86. This is a computational pocket signal, not binding validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.66. Review the complete evidence below

Risks to review

Human similarity Top human hit identity: 59.164%. This target also has a predicted binding pocket (FPocket 0.86) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 163 of 4744 screened genomes (3.4%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.86) — check the ligand evidence before deprioritizing on off-target risk alone.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.
Terms and data sources used on 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 Target 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.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
Hit
Human identity (%)
59.164 Lower values reduce human off-target concern.
Human E-value
3.23e-119
Gut microbiome similarity
3.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
77.814 Higher values support similarity to known essential genes.
DEG E-value
1.65e-166 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Unknown

Structure confidence

ColabFold pLDDT
97.17 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

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.

FPocket 0.863
Structure A0A0H3GWA1
Pocket Pocket 4
P2Rank 0.662
Structure A0A0H3GWA1
Pocket Pocket 1
ColabFold model
FPocket 0.781 · Pocket 3
P2Rank 0.603 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 163 / 4744 genomes with a hit
Prevalence 3.4%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GWA1

Sequence

Primary amino-acid sequence viewer.

MKVAVLGAAGGIGQALALLLKTQLPSGSELSLYDIAPVTPGVAVDLSHIPTDVKIKGFSGEDATPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVQQIAKTCPQACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLFGVTTLDIIRSNTFVAELKGKSATEVEVPVIGGHSGVTILPLLSQIPGVSFSDQEIADLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLVRAMQGEKGVVECAYVEGDGHYARFFSQPLLLGKNGVEERQSIGKLSAFEQQALEGMLDTLKKDIALGEDFVNK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • 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.
  • GO:0006108 The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle.
  • GO:0019752 The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
  • GO:0030060 Catalysis of the reaction: (S)-malate + NAD+ = oxaloacetate + NADH + H+.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0006099 A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
  • GO:0016615 Catalysis of the reversible conversion of pyruvate or oxaloacetate to malate.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

29 records
Show feature table
Start End DB Term Name
146 158 ProSitePatterns PS00068 Malate dehydrogenase active site signature.
146 158 InterPro IPR001252 Malate dehydrogenase, active site
1 311 Hamap MF_01516 Malate dehydrogenase [mdh].
1 311 InterPro IPR023958 Malate dehydrogenase, type 1, bacterial
1 2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
146 311 SUPERFAMILY SSF56327 LDH C-terminal domain-like
146 311 InterPro IPR015955 Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal
1 310 CDD cd01337 MDH_glyoxysomal_mitochondrial
1 310 InterPro IPR010097 Malate dehydrogenase, type 1
13 17 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
3 12 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 146 Gene3D G3DSA:3.40.50.720 -
1 312 PANTHER PTHR11540 MALATE AND LACTATE DEHYDROGENASE
147 310 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain
147 310 InterPro IPR022383 Lactate/malate dehydrogenase, C-terminal
2 311 NCBIfam TIGR01772 malate dehydrogenase
2 311 InterPro IPR010097 Malate dehydrogenase, type 1
1 145 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
1 145 InterPro IPR036291 NAD(P)-binding domain superfamily
1 146 FunFam G3DSA:3.40.50.720:FF:000017 Malate dehydrogenase
18 312 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
147 312 FunFam G3DSA:3.90.110.10:FF:000001 Malate dehydrogenase
1 17 Phobius SIGNAL_PEPTIDE Signal peptide region
1 145 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain
1 145 InterPro IPR001236 Lactate/malate dehydrogenase, N-terminal
147 312 Gene3D G3DSA:3.90.110.10 -
147 312 InterPro IPR015955 Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal
1 309 PIRSF PIRSF000102 Lac_mal_DH
1 309 InterPro IPR001557 L-lactate/malate dehydrogenase

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.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #4
0.863
Likely same site as P2Rank 2 5.1 Å 14 shared residues 74% of smaller site
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.662
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Surrounding area
Site 2 P2Rank #2
0.415
Likely same site as FPocket 4 5.1 Å 14 shared residues 74% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.048
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Surrounding area
Site 4 P2Rank #4
0.01
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Surrounding area
Residue sets
UniProt: Active site:177-177 Proton acceptor
UniProt: Binding site:117-119
UniProt: Binding site:119-119
UniProt: Binding site:153-153
UniProt: Binding site:227-227
UniProt: Binding site:34-34
UniProt: Binding site:7-13
UniProt: Binding site:81-81
UniProt: Binding site:87-87
UniProt: Binding site:94-94
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GWA1
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_02981
ColabFold — — full sequence — Loaded

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.

54 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 4 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
6V0 PDB via homolog 665.4 Da · LogP -3.03 · TPSA 317.6 Open detail RCSB PDB
LMR PDB via homolog Detail RCSB PDB
OAA PDB via homolog Detail RCSB PDB
PYR PDB via homolog Detail RCSB PDB
ZINC1532902 ZINC proposed compound · Tanimoto 0.700 Detail ZINC

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
6V0 RCSB PDB
5KKA
P61889 665.4 Da LogP -3.03 TPSA 317.6 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
LMR RCSB PDB
2DFD
P40926 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)O)C(=O)O
OAA RCSB PDB
5ZI4
P32419 131.1 Da LogP -2.22 TPSA 94.5 ✓ Ro5 ✓ Clean C(C(=O)C(=O)O)C(=O)[O-]
PYR RCSB PDB
1IE3
P61889 88.1 Da LogP -0.34 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=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.