KpATCC43816 Protein target profile

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

Accession: VK055_2386

Gene: dapD AIK80983.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GMV1

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Length 274

Pocket druggability (P2Rank · AlphaFold DB model) 0.188

Metabolic reactions 1

Chokepoint No

Direct ligand evidence 0 55 total records

Functional annotation 1 EC 6 GO

Target summary

Promising target candidate with multiple supporting evidence streams.

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

Main supporting evidence

Central metabolic position More central than 97.9% 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. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. 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: 4.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 98.905 Higher values support similarity to known essential genes.
DEG E-value: 0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 95.54 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) 0.188

Structure A0A0H3GMV1

Pocket Pocket 1

Druggability (FPocket) 0.532

Structure A0A0H3GMV1

Pocket Pocket 14

ColabFold model

P2Rank 0.211 · Pocket 1

FPocket 0.687 · Pocket 17

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 230 / 4744 genomes with a hit

Prevalence 4.8%

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 97.9% of genes in this genome, no human homolog detected.

Relative network centrality 97.9% more central than 97.9% of genes in this genome

Chokepoint Not a chokepoint

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MQQLQNVIESAFERRADITPANVDTVTREAVNQVIALLDSGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNQVIDGAESRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFIARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTKIYDRETGEVFYGRVPAGSVVVSGNLPSKDGKYSLYCAVIVKKVDAKTRGKVGINELLRTID

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization: Cytoplasmic

Enzyme Commission (EC)

2.3.1.117

Gene Ontology (GO)

GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
GO:0008666 Catalysis of the reaction: (S)-2,3,4,5-tetrahydrodipicolinate + H2O + succinyl-CoA = L-2-succinylamino-6-oxopimelate + CoA.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0016779 Catalysis of the transfer of a nucleotidyl group from one compound (donor) to another (acceptor).
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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
1	273	PANTHER	PTHR19136	MOLYBDENUM COFACTOR GUANYLYLTRANSFERASE
1	256	SUPERFAMILY	SSF51161	Trimeric LpxA-like enzymes
1	256	InterPro	IPR011004	Trimeric LpxA-like superfamily
134	162	ProSitePatterns	PS00101	Hexapeptide-repeat containing-transferases signature.
134	162	InterPro	IPR018357	Hexapeptide transferase, conserved site
88	256	FunFam	G3DSA:2.160.10.10:FF:000004	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
3	273	NCBIfam	TIGR00965	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
3	273	InterPro	IPR005664	Tetrahydrodipicolinate N-succinyltransferase, transferase hexapeptide repeat family
102	239	CDD	cd03350	LbH_THP_succinylT
1	70	Gene3D	G3DSA:1.10.166.10	-
1	70	InterPro	IPR037133	Tetrahydrodipicolinate-N-succinyltransferase, N-terminal domain superfamily
88	256	Gene3D	G3DSA:2.160.10.10	Hexapeptide repeat proteins
1	272	Hamap	MF_00811	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase [dapD].
1	272	InterPro	IPR005664	Tetrahydrodipicolinate N-succinyltransferase, transferase hexapeptide repeat family
3	69	Pfam	PF14805	Tetrahydrodipicolinate N-succinyltransferase N-terminal
3	69	InterPro	IPR023180	Tetrahydrodipicolinate-N-succinyltransferase, chain A, domain 1
175	209	Pfam	PF14602	Hexapeptide repeat of succinyl-transferase
175	209	InterPro	IPR001451	Hexapeptide repeat

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

0.188

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Surrounding area

Pocket 2 P2Rank #2

0.091

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Surrounding area

Pocket 3 P2Rank #3

0.03

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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #14

0.532

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Surrounding area

Residue sets

UniProt: Binding site:104-104

UniProt: Binding site:141-141

Binding pockets · P2Rank

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

Pocket 1 P2Rank #1

0.211

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Surrounding area

Pocket 2 P2Rank #2

0.053

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Surrounding area

Pocket 3 P2Rank #3

0.032

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Surrounding area

Pocket 4 P2Rank #4

0.02

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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_A0A0H3GMV1	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_2386	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.

55 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 50 similarity-based ZINC candidates

Best available ligand signal

26P PDB via homolog 189.2 Da · LogP -0.78 · TPSA 117.7 Open detail RCSB PDB

NPI PDB via homolog Detail RCSB PDB

PML PDB via homolog Detail RCSB PDB

SCA PDB via homolog Detail RCSB PDB

SCO 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
26P RCSB PDB	3TDT	P56220	189.2 Da LogP -0.78 TPSA 117.7	✓ Ro5	✓ Clean	`C(C[C@@H](C(=O)O)N)CC(=O)C(=O)O`
NPI RCSB PDB	1KGQ	P56220	175.2 Da LogP 0.04 TPSA 100.6	✓ Ro5	✓ Clean	`C(CCC(=O)O)C[C@@H](C(=O)O)N`
PML RCSB PDB	1KGT	P56220	160.2 Da LogP 1.11 TPSA 74.6	✓ Ro5	✓ Clean	`C(CCC(=O)O)CCC(=O)O`
SCA RCSB PDB	1KGT	P56220	867.6 Da LogP -1.47 TPSA 400.9	3 viol.	✓ Clean	`CC(C)(CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H](…`
SCO RCSB PDB	1KGQ	P56220	850.6 Da LogP -2.61 TPSA 413.0	3 viol.	✓ Clean	`CC(C)(CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H](…`

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
ZINC1529497 ZINC	1.000	230.3 Da LogP 3.06 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCC(=O)O`
ZINC1531045 ZINC	1.000	202.2 Da LogP 2.28 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)O`
ZINC1593115 ZINC	1.000	216.3 Da LogP 2.67 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCC(=O)O`
ZINC1700020 ZINC	1.000	244.3 Da LogP 3.45 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCC(=O)O`
ZINC3860440 ZINC	1.000	258.4 Da LogP 3.84 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCC(=O)O`
ZINC3861298 ZINC	1.000	286.4 Da LogP 4.62 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCC(=O)O`
ZINC5113062 ZINC	1.000	272.4 Da LogP 4.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCC(=O)O`
ZINC2106542 ZINC	0.955	245.3 Da LogP 1.99 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCCCCCC(=O)O)C(=O)O`
ZINC2106543 ZINC	0.955	245.3 Da LogP 1.99 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCCCCCC(=O)O)C(=O)O`
ZINC2108713 ZINC	0.955	217.3 Da LogP 1.21 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCCCC(=O)O)C(=O)O`
ZINC2108714 ZINC	0.955	217.3 Da LogP 1.21 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCCCC(=O)O)C(=O)O`
ZINC26897400 ZINC	0.800	286.4 Da LogP 3.41 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC(=O)CCCCCCC(=O)O`
ZINC3074813 ZINC	0.800	258.3 Da LogP 2.63 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCC(=O)CCCCCC(=O)O`
ZINC34423725 ZINC	0.800	342.5 Da LogP 4.97 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)CCCCCCCCC(=O)O`
ZINC4822898 ZINC	0.800	272.3 Da LogP 3.02 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC(=O)CCCCCC(=O)O`
ZINC4822900 ZINC	0.800	300.4 Da LogP 3.80 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)CCCCCC(=O)O`
ZINC3055005 ZINC	0.762	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	0.762	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	0.762	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC13433578 ZINC	0.750	201.3 Da LogP 1.68 TPSA 80.4	✓ Ro5	✓ Clean	`NC(=O)CCCCCCCCC(=O)O`
ZINC14510370 ZINC	0.750	244.4 Da LogP 3.74 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCO`
ZINC1531061 ZINC	0.750	216.3 Da LogP 2.96 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCO`
ZINC1610426 ZINC	0.750	230.3 Da LogP 3.35 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCO`
ZINC2168567 ZINC	0.750	202.3 Da LogP 2.57 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCO`
ZINC3074815 ZINC	0.750	230.3 Da LogP 1.85 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCC(=O)CCCC(=O)O`
ZINC3861297 ZINC	0.750	272.4 Da LogP 4.52 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCCO`
ZINC4284502 ZINC	0.750	258.4 Da LogP 4.13 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCO`
ZINC5287109 ZINC	0.750	286.5 Da LogP 4.91 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCCCO`
ZINC2508031 ZINC	0.733	230.3 Da LogP 1.85 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCC(=O)CCCCC(=O)O`
ZINC1555366 ZINC	0.727	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	0.727	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	0.727	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	0.727	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	0.727	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	0.727	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC12954423 ZINC	0.706	232.4 Da LogP 3.90 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCS`
ZINC13357569 ZINC	0.706	243.4 Da LogP 3.71 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCC(=O)O`
ZINC138216182 ZINC	0.706	293.2 Da LogP 4.76 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCBr`
ZINC1529498 ZINC	0.706	200.3 Da LogP 3.99 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)O`
ZINC1530417 ZINC	0.706	228.4 Da LogP 4.77 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)O`
ZINC1628119 ZINC	0.706	214.3 Da LogP 4.38 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)O`
ZINC1763117 ZINC	0.706	201.3 Da LogP 2.54 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCC(=O)O`
ZINC1841307 ZINC	0.706	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCCC(=O)O`
ZINC1845839 ZINC	0.706	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCC(=O)O`
ZINC2164257 ZINC	0.706	218.4 Da LogP 3.51 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCS`
ZINC22048354 ZINC	0.706	229.4 Da LogP 3.32 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCC(=O)O`
ZINC34552398 ZINC	0.706	257.4 Da LogP 4.10 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCC(=O)O`
ZINC35465466 ZINC	0.706	244.3 Da LogP 2.24 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCC(=O)CCC(=O)O`
ZINC5855130 ZINC	0.706	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCCCC(=O)O`
ZINC90745150 ZINC	0.706	260.4 Da LogP 4.68 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCS`

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 A0A0H3GMV1

Pathways

KEGG R04365 BioCyc TETHYDPICSUCC-RXN