KpKP13 Protein target profile
Mandelate racemase/muconate lactonizing enzyme family protein
Accession: KP13_03161
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.
Main supporting evidence
Risks to review
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 modelP2Rank'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.
Sequence
Primary amino-acid sequence viewer.
MKIESVNVTVFQYPTRRVSDSAGHSHPGVESMAKMAMLTITADDGAQGFSFAPPEVVRPFVVNTFFRKVLVGQDPFNRERIWQDLNHWQRGSAHQLTERALSFVEQALWDLIGRSLKMPVYKLLGGYRDTVPAYGSTMCGDDLPGGLSTPEEYAAFAEKLVARGYKAIKLHTWMPPISFAPNPKMDIKACAAVREAVGPDIDLMIDGYHWYSRAEALWIGKELEKLNFAWFEEPMEEDSMSSYAWLAENLSIPIVGPESFGGKHHMRAEWVKAGACDILRAGANGVGGITPTMKVAALAESFGMDCEVHGNGAASLAVVGAIRNCRWYERGLLHPFLDYDEPAAYLNSIVDPMDDQGFVHLSQRPGLGEDINFAYIEANTVSHD
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
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.
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.
How colors and pocket overlays are used
Pocket details Inspect a specific pocket, or open the full viewer
- Method
- -
- Score
- -
- Visible layer
- -
- Residues
- -
- Pocket properties
- -
Selecting a pocket opens its details and centers the viewer without clearing other active layers. Use Focus this pocket when you want to hide the rest; use Surface for the wider residue environment.
Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
All structural evidence
Structural evidence
0 + 2Experimental 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.
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 Target, 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 |
|---|---|---|---|---|---|---|
| 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
|
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 | 1.000 | 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 | 1.000 | 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
|
| ZINC1529628 ZINC | 1.000 | 274.3 Da LogP -1.32 TPSA 165.6 | 1 viol. | ✓ Clean |
N=C(N)NCCC[C@H](NC(=O)CCC(=O)O)C(=O)O
|
| ZINC1549593 ZINC | 1.000 | 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 | 1.000 | 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 | 1.000 | 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 | 1.000 | 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 | 1.000 | 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 | 1.000 | 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 | 0.846 | 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
|
| ZINC1866114950 ZINC | 0.844 | 260.3 Da LogP -0.06 TPSA 129.7 | ✓ Ro5 | ✓ Clean |
NCCCC[C@H](NC(=O)CCCC(=O)O)C(=O)O
|
| ZINC2383349774 ZINC | 0.838 | 330.4 Da LogP 0.24 TPSA 165.6 | 1 viol. | ✓ Clean |
N=C(N)NCCC[C@H](NC(=O)CCCCCCC(=O)O)C(=O)O
|
| ZINC1530138 ZINC | 0.806 | 217.3 Da LogP -0.97 TPSA 118.4 | ✓ Ro5 | ✓ Clean |
NCCCC[C@H](NC(=O)CCN)C(=O)O
|
| ZINC15261332 ZINC | 0.744 | 303.3 Da LogP -1.99 TPSA 191.6 | 1 viol. | ✓ Clean |
N=C(N)NCCC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O
|
| ZINC1576211 ZINC | 0.730 | 231.3 Da LogP -2.22 TPSA 154.3 | 1 viol. | ✓ Clean |
N=C(N)NCCC[C@H](NC(=O)CN)C(=O)O
|
| ZINC100008960 ZINC | 0.707 | 356.5 Da LogP 2.74 TPSA 128.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCC(=O)N[C@H](CCCNC(=N)N)C(=O)O
|
| ZINC70669861 ZINC | 0.707 | 356.5 Da LogP 2.74 TPSA 128.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCC(=O)N[C@@H](CCCNC(=N)N)C(=O)O
|
| ZINC85738396 ZINC | 0.707 | 384.6 Da LogP 3.52 TPSA 128.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCCC(=O)N[C@@H](CCCNC(=N)N)C(=O)O
|
| ZINC116981435 ZINC | 0.706 | 319.3 Da LogP -0.81 TPSA 179.0 | 1 viol. | ✓ Clean |
NCCCC[C@@H](NC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=O)O
|
| ZINC116981437 ZINC | 0.706 | 319.3 Da LogP -0.81 TPSA 179.0 | 1 viol. | ✓ Clean |
NCCCC[C@@H](NC(=O)N[C@H](CCC(=O)O)C(=O)O)C(=O)O
|
| ZINC116981440 ZINC | 0.706 | 319.3 Da LogP -0.81 TPSA 179.0 | 1 viol. | ✓ Clean |
NCCCC[C@H](NC(=O)N[C@H](CCC(=O)O)C(=O)O)C(=O)O
|
| ZINC40860752 ZINC | 0.706 | 319.3 Da LogP -0.81 TPSA 179.0 | 1 viol. | ✓ Clean |
NCCCC[C@H](NC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=O)O
|
| ZINC1847640 ZINC | 0.703 | 216.2 Da LogP -1.16 TPSA 128.3 | ✓ Ro5 | ✓ Clean |
CC(=O)N[C@@H](CCCNC(=N)N)C(=O)O
|
| ZINC2169795 ZINC | 0.703 | 216.2 Da LogP -1.16 TPSA 128.3 | ✓ Ro5 | ✓ Clean |
CC(=O)N[C@H](CCCNC(=N)N)C(=O)O
|
| ZINC13514809 ZINC | 0.694 | 404.4 Da LogP -1.77 TPSA 222.1 | 1 viol. | ✓ Clean |
NCCCC[C@H](NC(=O)CC[C@H](NC(=O)CC[C@H](N)C(=O)O…
|
| ZINC1722125 ZINC | 0.694 | 217.2 Da LogP -1.63 TPSA 154.3 | 1 viol. | ✓ Clean |
N=C(N)NCCC[C@H](NC(N)=O)C(=O)O
|
| ZINC4537126 ZINC | 0.694 | 217.2 Da LogP -1.63 TPSA 154.3 | 1 viol. | ✓ Clean |
N=C(N)NCCC[C@@H](NC(N)=O)C(=O)O
|
| ZINC1529261 ZINC | 0.684 | 304.3 Da LogP -1.39 TPSA 185.8 | 1 viol. | ✓ Clean |
N=C(N)NCCC[C@@H](N[C@@H](CCC(=O)O)C(=O)O)C(=O)O
|
| ZINC1529262 ZINC | 0.684 | 304.3 Da LogP -1.39 TPSA 185.8 | 1 viol. | ✓ Clean |
N=C(N)NCCC[C@@H](N[C@H](CCC(=O)O)C(=O)O)C(=O)O
|
| ZINC1529939 ZINC | 0.684 | 304.3 Da LogP -1.39 TPSA 185.8 | 1 viol. | ✓ Clean |
N=C(N)NCCC[C@H](N[C@@H](CCC(=O)O)C(=O)O)C(=O)O
|
| ZINC1529940 ZINC | 0.684 | 304.3 Da LogP -1.39 TPSA 185.8 | 1 viol. | ✓ Clean |
N=C(N)NCCC[C@H](N[C@H](CCC(=O)O)C(=O)O)C(=O)O
|
| ZINC1530510 ZINC | 0.684 | 246.3 Da LogP -1.23 TPSA 148.5 | 1 viol. | ✓ Clean |
N=C(N)NCCC[C@H](NCCC(=O)O)C(=O)O
|
| ZINC1530296 ZINC | 0.677 | 247.2 Da LogP -0.71 TPSA 141.0 | ✓ Ro5 | ✓ Clean |
O=C(O)CCC(=O)N[C@@H](CCC(=O)O)C(=O)O
|
| ZINC6783254 ZINC | 0.676 | 231.2 Da LogP 0.61 TPSA 103.7 | ✓ Ro5 | ✓ Clean |
CCCC[C@H](NC(=O)CCC(=O)O)C(=O)O
|
| ZINC6783285 ZINC | 0.676 | 231.2 Da LogP 0.61 TPSA 103.7 | ✓ Ro5 | ✓ Clean |
CCCC[C@@H](NC(=O)CCC(=O)O)C(=O)O
|
| ZINC113625226 ZINC | 0.676 | 272.4 Da LogP 2.05 TPSA 92.4 | ✓ Ro5 | ✓ Clean |
CCCCCCCC(=O)N[C@@H](CCCCN)C(=O)O
|
| ZINC28539131 ZINC | 0.676 | 328.5 Da LogP 3.61 TPSA 92.4 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCC(=O)N[C@@H](CCCCN)C(=O)O
|
| ZINC4403323 ZINC | 0.667 | 210.2 Da LogP -3.10 TPSA 138.4 | 1 viol. | ✓ Clean |
C[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)C(=O)O
|
| ZINC4403326 ZINC | 0.667 | 210.2 Da LogP -3.10 TPSA 138.4 | 1 viol. | ✓ Clean |
C[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)C(=O)O
|
| ZINC4403327 ZINC | 0.667 | 210.2 Da LogP -3.10 TPSA 138.4 | 1 viol. | ✓ Clean |
C[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)C(=O)O
|
| ZINC4403330 ZINC | 0.667 | 210.2 Da LogP -3.10 TPSA 138.4 | 1 viol. | ✓ Clean |
C[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)C(=O…
|
| ZINC1576188 ZINC | 0.659 | 288.3 Da LogP -3.11 TPSA 183.4 | 1 viol. | ✓ Clean |
N=C(N)NCCC[C@H](NC(=O)CNC(=O)CN)C(=O)O
|
| ZINC5502067 ZINC | 0.659 | 288.3 Da LogP -3.11 TPSA 183.4 | 1 viol. | ✓ Clean |
N=C(N)NCCC[C@@H](NC(=O)CNC(=O)CN)C(=O)O
|
| ZINC2516165 ZINC | 0.649 | 275.3 Da LogP -1.12 TPSA 155.7 | ✓ Ro5 | ✓ Clean |
NCCCC[C@H](NC(=O)[C@@H](N)CCC(=O)O)C(=O)O
|
| ZINC58123315 ZINC | 0.645 | 376.3 Da LogP -1.36 TPSA 207.4 | 1 viol. | ✓ Clean |
O=C(O)CC[C@H](NC(=O)CCC(=O)N[C@@H](CCC(=O)O)C(=…
|
| ZINC58123320 ZINC | 0.645 | 376.3 Da LogP -1.36 TPSA 207.4 | 1 viol. | ✓ Clean |
O=C(O)CC[C@H](NC(=O)CCC(=O)N[C@H](CCC(=O)O)C(=O…
|
| ZINC58123326 ZINC | 0.645 | 376.3 Da LogP -1.36 TPSA 207.4 | 1 viol. | ✓ Clean |
O=C(O)CC[C@@H](NC(=O)CCC(=O)N[C@H](CCC(=O)O)C(=…
|
| ZINC39798595 ZINC | 0.644 | 360.4 Da LogP -2.87 TPSA 220.7 | 1 viol. | ✓ Clean |
N=C(N)NCCC[C@H](N)C(=O)NCC(=O)N[C@@H](CCC(=O)O)…
|
| ZINC1731788 ZINC | 0.643 | 303.3 Da LogP -1.99 TPSA 191.6 | 1 viol. | ✓ Clean |
N=C(N)NCCC[C@H](N)C(=O)N[C@@H](CCC(=O)O)C(=O)O
|
| ZINC1731789 ZINC | 0.643 | 303.3 Da LogP -1.99 TPSA 191.6 | 1 viol. | ✓ Clean |
N=C(N)NCCC[C@@H](N)C(=O)N[C@@H](CCC(=O)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.
Cross-references
External database identifiers for this protein, its structures, ligands, and metabolic reactions.