KpKP13 Protein target profile

Mandelate racemase/muconate lactonizing enzyme family protein

Accession: KP13_03161

Gene: AHE43623.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GVB7
Length 384
Pocket druggability (P2Rank · AlphaFold DB model) 0.949
Direct ligand evidence 0 60 total records
Functional annotation 0 EC 3 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing 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 (%)
25.362 Lower values reduce human off-target concern.
Human E-value
1.75e-06
Gut microbiome similarity
0.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
97.98 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.949
Structure A0A0H3GVB7
Pocket Pocket 1
Druggability (FPocket) 0.542
Structure A0A0H3GVB7
Pocket Pocket 11
ColabFold model
P2Rank 0.832 · Pocket 1
FPocket 0.531 · Pocket 6
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 32 / 4744 genomes with a hit
Prevalence 0.7%

Sequence

Primary amino-acid sequence viewer.

MKIESVNVTVFQYPTRRVSDSAGHSHPGVESMAKMAMLTITADDGAQGFSFAPPEVVRPFVVNTFFRKVLVGQDPFNRERIWQDLNHWQRGSAHQLTERALSFVEQALWDLIGRSLKMPVYKLLGGYRDTVPAYGSTMCGDDLPGGLSTPEEYAAFAEKLVARGYKAIKLHTWMPPISFAPNPKMDIKACAAVREAVGPDIDLMIDGYHWYSRAEALWIGKELEKLNFAWFEEPMEEDSMSSYAWLAENLSIPIVGPESFGGKHHMRAEWVKAGACDILRAGANGVGGITPTMKVAALAESFGMDCEVHGNGAASLAVVGAIRNCRWYERGLLHPFLDYDEPAAYLNSIVDPMDDQGFVHLSQRPGLGEDINFAYIEANTVSHD

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

3
  • GO:0016836 Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0016052 The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
118 382 Gene3D G3DSA:3.20.20.120 -
118 382 InterPro IPR036849 Enolase-like, C-terminal domain superfamily
1 378 PANTHER PTHR13794 ENOLASE SUPERFAMILY, MANDELATE RACEMASE
1 378 InterPro IPR046945 L-rhamnonate dehydratase-like
150 253 SMART SM00922 MR_MLE_2
150 253 InterPro IPR013342 Mandelate racemase/muconate lactonizing enzyme, C-terminal
1 127 SUPERFAMILY SSF54826 Enolase N-terminal domain-like
1 127 InterPro IPR029017 Enolase-like, N-terminal
31 125 Pfam PF02746 Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
31 125 InterPro IPR013341 Mandelate racemase/muconate lactonizing enzyme, N-terminal domain
2 379 CDD cd03329 MR_like_4
1 116 Gene3D G3DSA:3.30.390.10 -
1 116 InterPro IPR029017 Enolase-like, N-terminal
113 381 SUPERFAMILY SSF51604 Enolase C-terminal domain-like
113 381 InterPro IPR036849 Enolase-like, C-terminal domain superfamily
153 372 Pfam PF13378 Enolase C-terminal domain-like
153 372 InterPro IPR029065 Enolase C-terminal domain-like

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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.949
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.064
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.041
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.002
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #11
0.542
Show in viewer
Surrounding area
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_A0A0H3GVB7
AlphaFold DB full sequence Viewing
ColabFold KP13_03161
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.

60 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 10 records from similar proteins
Structural ligands 10 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
AKG PDB via homolog 146.1 Da · LogP -0.50 · TPSA 91.7 Open detail RCSB PDB
CS2 PDB via homolog Detail RCSB PDB
DXL PDB via homolog Detail RCSB PDB
LGT PDB via homolog Detail RCSB PDB
LLH PDB via homolog Detail RCSB PDB

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
AKG RCSB PDB A0A0H3LT39 146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)C(=O)O
CS2 RCSB PDB Q9AAR4 196.2 Da LogP -3.49 TPSA 138.5 1 viol. ✓ Clean C([C@H]([C@H]([C@@H]([C@@H](C(=O)O)O)O)O)O)O
DXL RCSB PDB A0A0H3LT39 180.1 Da LogP -2.76 TPSA 135.3 ✓ Ro5 ✓ Clean [C@@H](C([C@@H](C(=O)O)O)O)(C(=O)O)O
LGT RCSB PDB Q8ZL58 210.1 Da LogP -3.40 TPSA 155.5 1 viol. ✓ Clean [C@@H]([C@H]([C@H](C(=O)O)O)O)([C@@H](C(=O)O)O)O
LLH RCSB PDB Q7CSI0 195.1 Da LogP -3.34 TPSA 147.3 1 viol. ✓ Clean [C@H]([C@H](C(=O)NO)O)([C@H](C(=O)O)O)O
LY9 RCSB PDB A0A0H3LT39 180.1 Da LogP -2.76 TPSA 135.3 ✓ Ro5 ✓ Clean [C@@H](C([C@H](C(=O)O)O)O)(C(=O)O)O
NSK RCSB PDB Q81IL5 246.3 Da LogP -0.45 TPSA 129.7 ✓ Ro5 ✓ Clean C(CCN)C[C@@H](C(=O)O)NC(=O)CCC(=O)O
SUG RCSB PDB Q81IL5 274.3 Da LogP -1.32 TPSA 165.6 1 viol. ✓ Clean C(C[C@@H](C(=O)O)NC(=O)CCC(=O)O)CNC(=N)N
TLA RCSB PDB Q7CSI0 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=O)O)O
XYH RCSB PDB Q7CSI0 194.1 Da LogP -4.68 TPSA 150.1 ✓ Ro5 ✓ Clean [C@H]([C@@H](C(=O)NO)O)([C@H](C(=O)[O-])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.

Cross-references

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