KpATCC43816 Protein target profile

diaminopimelate epimerase

Accession: VK055_3167

Gene: AIK81739.1 dapF 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GKE3

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Length 274

Pocket druggability (P2Rank · AlphaFold DB model) 0.764

Metabolic reactions 1

Chokepoint Yes

Direct ligand evidence 0 42 total records

Functional annotation 1 EC 4 GO

Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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

Main supporting evidence

Metabolic chokepoint Catalyzes a reaction that is the only producer or consumer of a metabolite in the imported metabolic model. Central metabolic position More central than 97.0% of genes in this genome. No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Review the complete evidence below

Risks to review

Evidence coverage

Core evidence streams are available for this target.

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: No hit
Gut microbiome similarity: 4.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 95.255 Higher values support similarity to known essential genes.
DEG E-value: 0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 95.78 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) 0.764

Structure A0A0H3GKE3

Pocket Pocket 1

Druggability (FPocket) 0.203

Structure A0A0H3GKE3

Pocket Pocket 10

ColabFold model

P2Rank 0.378 · Pocket 1

FPocket 0.246 · Pocket 10

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 200 / 4744 genomes with a hit

Prevalence 4.2%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Attractive metabolic target: catalyzes a producing & consuming chokepoint reaction in D-Amino acid metabolism, no isoenzyme backup detected, more central than 97.0% of genes in this genome, no human homolog detected.

Relative network centrality 97.0% more central than 97.0% of genes in this genome

Chokepoint Chokepoint gene

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPDLDFHYRIFNADGSEVSQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLSVTEDDLVRVNMGEPNFEPSQVPFRANKAEKTYIMRAAEQTVLCGVVSMGNPHCVIQVDDVDTAAVETLGPVMESHERFPERANIGFMQVVGRSHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAETVRVELPGGRLDIAWKGPGQPLFMTGPAAHVYDGFIHL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization: Cytoplasmic

Enzyme Commission (EC)

5.1.1.7

Gene Ontology (GO)

GO:0008837 Catalysis of the reaction: LL-2,6-diaminopimelate = meso-2,6-diaminopimelate.
GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

17 records

Show feature table

Start	End	DB	Term	Name
1	274	Hamap	MF_00197	Diaminopimelate epimerase [dapF].
1	274	InterPro	IPR001653	Diaminopimelate epimerase, DapF
2	270	Gene3D	G3DSA:3.10.310.10	Diaminopimelate Epimerase; Chain A, domain 1
2	118	FunFam	G3DSA:3.10.310.10:FF:000001	Diaminopimelate epimerase
2	273	SUPERFAMILY	SSF54506	Diaminopimelate epimerase-like
115	261	Gene3D	G3DSA:3.10.310.10	Diaminopimelate Epimerase; Chain A, domain 1
3	123	Pfam	PF01678	Diaminopimelate epimerase
3	123	InterPro	IPR001653	Diaminopimelate epimerase, DapF
152	266	Pfam	PF01678	Diaminopimelate epimerase
152	266	InterPro	IPR001653	Diaminopimelate epimerase, DapF
64	78	ProSitePatterns	PS01326	Diaminopimelate epimerase signature.
64	78	InterPro	IPR018510	Diaminopimelate epimerase, active site
1	273	NCBIfam	TIGR00652	diaminopimelate epimerase
1	273	InterPro	IPR001653	Diaminopimelate epimerase, DapF
2	273	PANTHER	PTHR31689	DIAMINOPIMELATE EPIMERASE, CHLOROPLASTIC
2	273	InterPro	IPR001653	Diaminopimelate epimerase, DapF
119	261	FunFam	G3DSA:3.10.310.10:FF:000002	Diaminopimelate epimerase

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

0.764

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Surrounding area

Pocket 2 P2Rank #2

0.005

Show in viewer

Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #10

0.203

Show in viewer

Surrounding area

Residue sets

UniProt: Active site:217-217 Proton acceptor

UniProt: Active site:73-73

UniProt: Binding site:11-11

UniProt: Binding site:157-157

UniProt: Binding site:190-190

UniProt: Binding site:208-209

UniProt: Binding site:218-219

UniProt: Binding site:44-44

UniProt: Binding site:64-64

UniProt: Binding site:74-75

UniProt: Site:159-159 Could be important to modulate the pK values of the two catalytic cysteine residues

UniProt: Site:208-208 Could be important to modulate the pK values of the two catalytic cysteine residues

UniProt: Site:268-268 Important for dimerization

Residue sets

UniProt: Active site:217-217 Proton acceptor

UniProt: Active site:73-73

UniProt: Binding site:11-11

UniProt: Binding site:157-157

UniProt: Binding site:190-190

UniProt: Binding site:208-209

UniProt: Binding site:218-219

UniProt: Binding site:44-44

UniProt: Binding site:64-64

UniProt: Binding site:74-75

UniProt: Site:159-159 Could be important to modulate the pK values of the two catalytic cysteine residues

UniProt: Site:208-208 Could be important to modulate the pK values of the two catalytic cysteine residues

UniProt: Site:268-268 Important for dimerization

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_A0A0H3GKE3	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_3167	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.

42 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 5 records from similar proteins

Structural ligands 5 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 37 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

DTT PDB via homolog Detail RCSB PDB

TLA PDB via homolog Detail RCSB PDB

ZDP PDB via homolog Detail RCSB PDB

ZDR PDB via homolog Detail RCSB PDB

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	5M47	Q8NP73	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`
DTT RCSB PDB	3FVE	P9WP19	154.3 Da LogP -0.43 TPSA 40.5	✓ Ro5	✓ Clean	`C([C@@H]([C@H](CS)O)O)S`
TLA RCSB PDB	5YGU	P0A6K1	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@@H]([C@H](C(=O)O)O)(C(=O)O)O`
ZDP RCSB PDB	2GKE	P44859	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`C[C@](CCC[C@@H](C(=O)O)N)(C(=O)O)N`
ZDR RCSB PDB	2GKJ	P44859	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`C[C@@](CCC[C@@H](C(=O)O)N)(C(=O)O)N`

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	0.692	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	0.692	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	0.692	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`
ZINC1549593 ZINC	0.692	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	0.692	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	0.692	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	0.692	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	0.692	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	0.692	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`
ZINC1560405156 ZINC	0.588	208.1 Da LogP -1.79 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)/C(O)=C(\O)[C@H](O)[C@H](O)C(=O)O`
ZINC1560405157 ZINC	0.588	208.1 Da LogP -1.79 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)/C(O)=C(/O)[C@H](O)[C@H](O)C(=O)O`
ZINC1555366 ZINC	0.556	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	0.556	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	0.556	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	0.556	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	0.556	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	0.556	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC100300547 ZINC	0.548	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCC[C@@](C)(N)C(=O)O`
ZINC1652265 ZINC	0.548	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCC[C@](C)(N)C(=O)O`
ZINC1570993 ZINC	0.516	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCC[C@H](N)C(=O)O`
ZINC1570999 ZINC	0.516	229.4 Da LogP 3.32 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCC[C@H](N)C(=O)O`
ZINC1620974 ZINC	0.516	243.4 Da LogP 3.71 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[C@H](N)C(=O)O`
ZINC1742220 ZINC	0.516	201.3 Da LogP 2.54 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCC[C@H](N)C(=O)O`
ZINC2035155 ZINC	0.516	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCC[C@@H](N)C(=O)O`
ZINC2035157 ZINC	0.516	201.3 Da LogP 2.54 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCC[C@@H](N)C(=O)O`
ZINC2037129 ZINC	0.516	243.4 Da LogP 3.71 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[C@@H](N)C(=O)O`
ZINC43531622 ZINC	0.516	271.4 Da LogP 4.49 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC[C@H](N)C(=O)O`
ZINC43531626 ZINC	0.516	271.4 Da LogP 4.49 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC[C@@H](N)C(=O)O`
ZINC8437446 ZINC	0.516	229.4 Da LogP 3.32 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCC[C@@H](N)C(=O)O`
ZINC2382564 ZINC	0.514	217.3 Da LogP 0.91 TPSA 89.6	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)CCC[C@H](N)C(=O)O`
ZINC71613550 ZINC	0.514	217.3 Da LogP 0.91 TPSA 89.6	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)CCC[C@@H](N)C(=O)O`
ZINC1529331 ZINC	0.500	206.1 Da LogP -2.21 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)[C@H](C(=O)O)[C@@H](O)C(=O)O`
ZINC1529332 ZINC	0.500	206.1 Da LogP -2.21 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)[C@H](C(=O)O)[C@H](O)C(=O)O`
ZINC1529333 ZINC	0.500	206.1 Da LogP -2.21 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)[C@@H](C(=O)O)[C@@H](O)C(=O)O`
ZINC1529334 ZINC	0.500	206.1 Da LogP -2.21 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)[C@@H](C(=O)O)[C@H](O)C(=O)O`
ZINC2140007 ZINC	0.500	225.2 Da LogP 0.14 TPSA 120.9	✓ Ro5	✓ Clean	`C[C@@](N)(CCCCP(=O)(O)O)C(=O)O`
ZINC2140009 ZINC	0.500	225.2 Da LogP 0.14 TPSA 120.9	✓ Ro5	✓ Clean	`C[C@](N)(CCCCP(=O)(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.

Sequence

UniProt A0A0H3GKE3

Pathways

KEGG R02735 BioCyc DIAMINOPIMEPIM-RXN