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 (%)
- 42.857 Lower values reduce human off-target concern.
- Human E-value
- 2.76e-07
- Gut microbiome similarity
- 4.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.
Essentiality
- Essential (DEG)
- Y
- DEG identity (%)
- 92.0 Higher values support similarity to known essential genes.
- DEG E-value
- 0.0 Smaller values mean stronger essential-gene similarity.
Localization
- Localization
- Unknown
Structure confidence
- ColabFold pLDDT
- 97.08 0-100 confidence; >70 supports local structural interpretation.
Binding-site evidence
AlphaFold DB / UniProt modelThe 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.
Cross-references
External database identifiers for this protein, its structures, ligands, and metabolic reactions.
Sequence
Sequence
Primary amino-acid sequence viewer.
MSCPVIELAQQLIRRPSLSPDDAGCQALMIERLRAIGFTVEPMDFGDTQNFWAWRGHGETLAFAGHTDVVPAGDADRWINPPFEPTIRDGMLFGRGAADMKGSLAAMVVATERFVAQYPNHRGRLAFLITSDEEASAKNGTVKVVETLMARNERLDYCLVGEPSSTEVVGDVVKNGRRGSLTCNLTIHGVQGHVAYPHLADNPVHRAAPMLAELVNIEWDKGNEFFPPTSMQIANVQSGTGSNNVIPGDMFVQFNFRFSTELTDEMIKSRVIALLEKYQLRYSVEWWLSGQPFLTGRGKLVDAVVNAIEHYNEIKPQLLTNGGTSDGRFIARMGAQVVELGPVNATIHKINECVNAADLQLLARMYQRVMEQLVA
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Enzyme Commission (EC)
1Gene Ontology (GO)
8- GO:0009014 Catalysis of the reaction: N-succinyl-LL-2,6-diaminopimelate + H2O = LL-2,6-diaminopimelate + succinate.
- GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
- GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
- GO:0008777 Catalysis of the reaction: N2-acetyl-L-ornithine + H2O = acetate + L-ornithine.
- GO:0050897 Binding to a cobalt ion (Co2+).
- GO:0008270 Binding to a zinc ion (Zn).
- GO:0019877 OBSOLETE. The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.
- GO:0006526 The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 256 | 375 | Gene3D | G3DSA:3.40.630.10 | Zn peptidases |
| 61 | 70 | ProSitePatterns | PS00758 | ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. |
| 61 | 70 | InterPro | IPR001261 | ArgE/DapE/ACY1/CPG2/YscS, conserved site |
| 179 | 289 | FunFam | G3DSA:3.30.70.360:FF:000011 | Succinyl-diaminopimelate desuccinylase |
| 255 | 375 | FunFam | G3DSA:3.40.630.10:FF:000010 | Succinyl-diaminopimelate desuccinylase |
| 3 | 244 | Gene3D | G3DSA:3.40.630.10 | Zn peptidases |
| 6 | 373 | NCBIfam | TIGR01246 | succinyl-diaminopimelate desuccinylase |
| 6 | 373 | InterPro | IPR005941 | Succinyl-diaminopimelate desuccinylase, proteobacteria |
| 3 | 244 | FunFam | G3DSA:3.40.630.10:FF:000005 | Succinyl-diaminopimelate desuccinylase |
| 5 | 373 | PANTHER | PTHR43808 | ACETYLORNITHINE DEACETYLASE |
| 97 | 136 | ProSitePatterns | PS00759 | ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. |
| 97 | 136 | InterPro | IPR001261 | ArgE/DapE/ACY1/CPG2/YscS, conserved site |
| 62 | 371 | Pfam | PF01546 | Peptidase family M20/M25/M40 |
| 62 | 371 | InterPro | IPR002933 | Peptidase M20 |
| 175 | 280 | Pfam | PF07687 | Peptidase dimerisation domain |
| 175 | 280 | InterPro | IPR011650 | Peptidase M20, dimerisation domain |
| 6 | 370 | CDD | cd03891 | M20_DapE_proteobac |
| 3 | 375 | Hamap | MF_01690 | Succinyl-diaminopimelate desuccinylase [dapE]. |
| 3 | 375 | InterPro | IPR005941 | Succinyl-diaminopimelate desuccinylase, proteobacteria |
| 179 | 287 | SUPERFAMILY | SSF55031 | Bacterial exopeptidase dimerisation domain |
| 179 | 287 | InterPro | IPR036264 | Bacterial exopeptidase dimerisation domain |
| 5 | 373 | SUPERFAMILY | SSF53187 | Zn-dependent exopeptidases |
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 · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Residue sets
Binding pockets · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
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_A0A0H3H1C2
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
KP13_03831
|
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 |
|---|---|---|---|---|---|---|
| API RCSB PDB | P44514 | 190.2 Da LogP -1.02 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
C(C[C@H](C(=O)O)N)C[C@@H](C(=O)O)N
|
|
| BES RCSB PDB | Q96KP4 | 308.4 Da LogP 0.53 TPSA 112.7 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@@H](C(=O)O)NC(=O)[C@H]([C@@H](Cc1ccccc…
|
|
| SIN RCSB PDB | P44514 | 118.1 Da LogP -0.06 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
C(CC(=O)O)C(=O)O
|
|
| X8Z RCSB PDB | Q9JYL2 | 217.3 Da LogP 0.63 TPSA 57.6 | ✓ Ro5 | ✓ Clean |
C[C@H](CS)C(=O)N1CCC[C@H]1C(=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 |
|---|---|---|---|---|---|
| ZINC11592554 ZINC | 1.000 | 308.4 Da LogP 0.53 TPSA 112.6 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@@H](NC(=O)[C@@H](O)[C@@H](N)Cc1ccccc1)…
|
| ZINC11592555 ZINC | 1.000 | 308.4 Da LogP 0.53 TPSA 112.6 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@@H](NC(=O)[C@H](O)[C@@H](N)Cc1ccccc1)C…
|
| ZINC11592556 ZINC | 1.000 | 308.4 Da LogP 0.53 TPSA 112.6 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@H](NC(=O)[C@H](O)[C@@H](N)Cc1ccccc1)C(…
|
| ZINC1532730 ZINC | 1.000 | 308.4 Da LogP 0.53 TPSA 112.6 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@@H](NC(=O)[C@@H](O)[C@H](N)Cc1ccccc1)C…
|
| ZINC1542895 ZINC | 1.000 | 308.4 Da LogP 0.53 TPSA 112.6 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@H](NC(=O)[C@@H](O)[C@H](N)Cc1ccccc1)C(…
|
| ZINC1558987 ZINC | 1.000 | 308.4 Da LogP 0.53 TPSA 112.6 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@@H](NC(=O)[C@H](O)[C@H](N)Cc1ccccc1)C(…
|
| ZINC20226 ZINC | 1.000 | 217.3 Da LogP 0.63 TPSA 57.6 | ✓ Ro5 | ✓ Clean |
C[C@H](CS)C(=O)N1CCC[C@@H]1C(=O)O
|
| ZINC2545165 ZINC | 1.000 | 308.4 Da LogP 0.53 TPSA 112.6 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@H](NC(=O)[C@H](O)[C@H](N)Cc1ccccc1)C(=…
|
| ZINC57000 ZINC | 1.000 | 217.3 Da LogP 0.63 TPSA 57.6 | ✓ Ro5 | ✓ Clean |
C[C@@H](CS)C(=O)N1CCC[C@H]1C(=O)O
|
| ZINC57001 ZINC | 1.000 | 217.3 Da LogP 0.63 TPSA 57.6 | ✓ Ro5 | ✓ Clean |
C[C@H](CS)C(=O)N1CCC[C@H]1C(=O)O
|
| ZINC57002 ZINC | 1.000 | 217.3 Da LogP 0.63 TPSA 57.6 | ✓ Ro5 | ✓ Clean |
C[C@@H](CS)C(=O)N1CCC[C@@H]1C(=O)O
|
| ZINC7996813 ZINC | 1.000 | 308.4 Da LogP 0.53 TPSA 112.6 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@H](NC(=O)[C@@H](O)[C@@H](N)Cc1ccccc1)C…
|
| ZINC3055005 ZINC | 0.882 | 204.2 Da LogP -0.63 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCCC[C@H](N)C(=O)O)C(=O)O
|
| ZINC3055007 ZINC | 0.882 | 204.2 Da LogP -0.63 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCCC[C@@H](N)C(=O)O)C(=O)O
|
| ZINC3055010 ZINC | 0.882 | 204.2 Da LogP -0.63 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@H](CCCC[C@@H](N)C(=O)O)C(=O)O
|
| ZINC1555366 ZINC | 0.833 | 232.3 Da LogP 0.15 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCCCCC[C@H](N)C(=O)O)C(=O)O
|
| ZINC1555367 ZINC | 0.833 | 232.3 Da LogP 0.15 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O
|
| ZINC1555369 ZINC | 0.833 | 232.3 Da LogP 0.15 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O
|
| ZINC1720127 ZINC | 0.833 | 218.3 Da LogP -0.24 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCCCC[C@H](N)C(=O)O)C(=O)O
|
| ZINC1720128 ZINC | 0.833 | 218.3 Da LogP -0.24 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCCCC[C@@H](N)C(=O)O)C(=O)O
|
| ZINC1720130 ZINC | 0.833 | 218.3 Da LogP -0.24 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@H](CCCCC[C@@H](N)C(=O)O)C(=O)O
|
| ZINC95572961 ZINC | 0.829 | 321.4 Da LogP 0.19 TPSA 104.5 | ✓ Ro5 | ✓ Clean |
CNC(=O)[C@H](CC(C)C)NC(=O)[C@@H](O)[C@H](N)Cc1c…
|
| ZINC1573805 ZINC | 0.810 | 324.4 Da LogP 0.24 TPSA 132.9 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@H](NC(=O)[C@@H](O)[C@H](N)Cc1ccc(O)cc1…
|
| ZINC17125728 ZINC | 0.810 | 324.4 Da LogP 0.24 TPSA 132.9 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@H](NC(=O)[C@@H](O)[C@@H](N)Cc1ccc(O)cc…
|
| ZINC17125733 ZINC | 0.810 | 324.4 Da LogP 0.24 TPSA 132.9 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@H](NC(=O)[C@H](O)[C@@H](N)Cc1ccc(O)cc1…
|
| ZINC5759636 ZINC | 0.810 | 324.4 Da LogP 0.24 TPSA 132.9 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@H](NC(=O)[C@H](O)[C@H](N)Cc1ccc(O)cc1)…
|
| ZINC2390944 ZINC | 0.756 | 278.4 Da LogP 1.17 TPSA 92.4 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@H](NC(=O)[C@@H](N)Cc1ccccc1)C(=O)O
|
| ZINC6049599 ZINC | 0.756 | 278.4 Da LogP 1.17 TPSA 92.4 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@@H](NC(=O)[C@@H](N)Cc1ccccc1)C(=O)O
|
| ZINC2391109 ZINC | 0.750 | 307.3 Da LogP 1.55 TPSA 103.7 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@H](NC(=O)[C@@H](Cc1ccccc1)C(=O)O)C(=O)O
|
| ZINC27727766 ZINC | 0.750 | 307.3 Da LogP 1.55 TPSA 103.7 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@@H](NC(=O)[C@@H](Cc1ccccc1)C(=O)O)C(=O…
|
| ZINC27727773 ZINC | 0.750 | 307.3 Da LogP 1.55 TPSA 103.7 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@@H](NC(=O)[C@H](Cc1ccccc1)C(=O)O)C(=O)O
|
| ZINC4899476 ZINC | 0.750 | 307.3 Da LogP 1.55 TPSA 103.7 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@H](NC(=O)[C@H](Cc1ccccc1)C(=O)O)C(=O)O
|
| ZINC27644022 ZINC | 0.721 | 294.4 Da LogP 0.29 TPSA 112.6 | ✓ Ro5 | ✓ Clean |
CCC[C@H](NC(=O)[C@H](O)[C@H](N)Cc1ccccc1)C(=O)O
|
| ZINC6003711 ZINC | 0.711 | 441.5 Da LogP 0.87 TPSA 141.7 | ✓ Ro5 | ✓ Clean |
CC(C)[C@H](NC(=O)[C@@H](O)[C@H](N)Cc1ccccc1)C(=…
|
| ZINC38212936 ZINC | 0.711 | 231.3 Da LogP 0.72 TPSA 46.6 | ✓ Ro5 | ✓ Clean |
COC(=O)[C@@H]1CCCN1C(=O)[C@H](C)CS
|
| ZINC111451008 ZINC | 0.703 | 231.3 Da LogP 1.06 TPSA 57.6 | ✓ Ro5 | ✓ Clean |
CSC[C@H](C)C(=O)N1CCC[C@H]1C(=O)O
|
| ZINC6036727 ZINC | 0.703 | 231.3 Da LogP 1.06 TPSA 57.6 | ✓ Ro5 | ✓ Clean |
CSC[C@@H](C)C(=O)N1CCC[C@H]1C(=O)O
|
| ZINC237154739 ZINC | 0.684 | 215.2 Da LogP 0.34 TPSA 66.8 | ✓ Ro5 | ✓ Clean |
COC[C@@H](C)C(=O)N1CCC[C@H]1C(=O)O
|
| ZINC237231340 ZINC | 0.684 | 215.2 Da LogP 0.34 TPSA 66.8 | ✓ Ro5 | ✓ Clean |
COC[C@H](C)C(=O)N1CCC[C@H]1C(=O)O
|
| ZINC4899773 ZINC | 0.682 | 391.5 Da LogP 1.70 TPSA 121.5 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@H](N)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](…
|
| ZINC1569745 ZINC | 0.674 | 278.4 Da LogP 1.17 TPSA 92.4 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@H](N)C(=O)N[C@@H](Cc1ccccc1)C(=O)O
|
| ZINC1569746 ZINC | 0.674 | 278.4 Da LogP 1.17 TPSA 92.4 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@@H](N)C(=O)N[C@@H](Cc1ccccc1)C(=O)O
|
| ZINC1569747 ZINC | 0.674 | 278.4 Da LogP 1.17 TPSA 92.4 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@H](N)C(=O)N[C@H](Cc1ccccc1)C(=O)O
|
| ZINC1569748 ZINC | 0.674 | 278.4 Da LogP 1.17 TPSA 92.4 | ✓ Ro5 | ✓ Clean |
CC(C)C[C@@H](N)C(=O)N[C@H](Cc1ccccc1)C(=O)O
|
| ZINC67664984 ZINC | 0.667 | 247.3 Da LogP 0.08 TPSA 74.7 | ✓ Ro5 | ✓ Clean |
C[C@H](C[S@](C)=O)C(=O)N1CCC[C@H]1C(=O)O
|
| ZINC67664986 ZINC | 0.667 | 247.3 Da LogP 0.08 TPSA 74.7 | ✓ Ro5 | ✓ Clean |
C[C@H](C[S@@](C)=O)C(=O)N1CCC[C@H]1C(=O)O
|
| ZINC2983230 ZINC | 0.659 | 320.4 Da LogP 1.35 TPSA 95.5 | ✓ Ro5 | ✓ Clean |
CC(=O)N[C@H](Cc1ccccc1)C(=O)N[C@@H](CC(C)C)C(=O…
|
| ZINC2983231 ZINC | 0.659 | 320.4 Da LogP 1.35 TPSA 95.5 | ✓ Ro5 | ✓ Clean |
CC(=O)N[C@H](Cc1ccccc1)C(=O)N[C@H](CC(C)C)C(=O)O
|
| ZINC2983232 ZINC | 0.659 | 320.4 Da LogP 1.35 TPSA 95.5 | ✓ Ro5 | ✓ Clean |
CC(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](CC(C)C)C(=…
|
| ZINC2983233 ZINC | 0.659 | 320.4 Da LogP 1.35 TPSA 95.5 | ✓ Ro5 | ✓ Clean |
CC(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@H](CC(C)C)C(=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.