Protein target profile

KP13_03831

Succinyl-diaminopimelate desuccinylase

Genome: KpKP13 Gene: AHE43315.1 dapE 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H1C2
Length 375
Pocket druggability 0.44
Direct ligand evidence 0 54 total records
Functional annotation 1 EC 8 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 (%)
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 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 0.44
Structure A0A0H3H1C2
Pocket Pocket 3
P2Rank 0.476
Structure A0A0H3H1C2
Pocket Pocket 1
ColabFold model
FPocket 0.442 · Pocket 1
P2Rank 0.458 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 200 / 4744 genomes with a hit
Prevalence 4.2%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MSCPVIELAQQLIRRPSLSPDDAGCQALMIERLRAIGFTVEPMDFGDTQNFWAWRGHGETLAFAGHTDVVPAGDADRWINPPFEPTIRDGMLFGRGAADMKGSLAAMVVATERFVAQYPNHRGRLAFLITSDEEASAKNGTVKVVETLMARNERLDYCLVGEPSSTEVVGDVVKNGRRGSLTCNLTIHGVQGHVAYPHLADNPVHRAAPMLAELVNIEWDKGNEFFPPTSMQIANVQSGTGSNNVIPGDMFVQFNFRFSTELTDEMIKSRVIALLEKYQLRYSVEWWLSGQPFLTGRGKLVDAVVNAIEHYNEIKPQLLTNGGTSDGRFIARMGAQVVELGPVNATIHKINECVNAADLQLLARMYQRVMEQLVA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene 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.

22 records
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.

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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 #3
0.44
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.476
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Surrounding area
Site 2 P2Rank #2
0.005
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.001
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Surrounding area
Residue sets
UniProt: Active site:133-133 Proton acceptor
UniProt: Active site:68-68
UniProt: Binding site:134-134
UniProt: Binding site:162-162
UniProt: Binding site:348-348
UniProt: Binding site:66-66
UniProt: Binding site:99-99
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_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.

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
API PDB via homolog 190.2 Da · LogP -1.02 · TPSA 126.6 Open detail RCSB PDB
BES PDB via homolog Detail RCSB PDB
SIN PDB via homolog Detail RCSB PDB
X8Z PDB via homolog Detail RCSB PDB
ZINC11592554 ZINC proposed compound · Tanimoto 1.000 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
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

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.