KpATCC43816 Protein target profile

CDP-diacylglycerol--serine O-phosphatidyltransferase

Accession: VK055_4593

Gene: AIK83127.1 pssA 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GTV1
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Length 451
Pocket druggability (P2Rank · AlphaFold DB model) 0.92
Metabolic reactions 1
Chokepoint Yes
Functional annotation 0 EC 5 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

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 96.6% of genes in this genome. No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Review the complete evidence below

Risks to review

Low human similarity A human hit was flagged, but identity is only 27.749% - a weak match, lower risk than a close homolog. This target also has a predicted binding pocket (P2Rank 0.92) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 131 of 4744 screened genomes (2.8%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.92) — check the ligand evidence before deprioritizing on off-target risk alone. Weak predicted binding pocket FPocket selected-pocket score 0.22.

Evidence gaps

No ligand evidence No experimental PDB ligands, measured ChEMBL bioactivity, or proposed ZINC compound records are available.
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 (%)
27.749 Lower values reduce human off-target concern.
Human E-value
2.11e-07
Gut microbiome similarity
2.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
95.26 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) 0.92
Structure A0A0H3GTV1
Pocket Pocket 1
Druggability (FPocket) 0.221
Structure A0A0H3GTV1
Pocket Pocket 12
ColabFold model
P2Rank 0.908 · Pocket 1
FPocket 0.262 · Pocket 14
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 131 / 4744 genomes with a hit
Prevalence 2.8%

Metabolic context

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

Explore metabolic network

Attractive metabolic target: catalyzes a producing chokepoint reaction in Glycerophospholipid metabolism, no isoenzyme backup detected, more central than 96.6% of genes in this genome.

Relative network centrality 96.6% more central than 96.6% of genes in this genome
Chokepoint Chokepoint gene
Pathways
Glycerophospholipid metabolism Glycine, serine and threonine metabolism
Catalyzed reaction

1 reaction mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MLSKFKRNKHQQHLAQLPKLSQSVDDVEFFYAPAEFREALLTRIAHATQRICIIALYLEQDDGGKGILQALYDAKRQRPELDVRVLVDWHRAQRGRIGAAASNTNADWYCRMANENPGVDIPVYGVPINTREALGVLHFKGFIIDDCVLYSGASLNDVYLHQHDKYRYDRYQCIRNGKMADIMFDWVDNNLVQGRGVNRLDRPDRPRSPEIKNDIRQYRQELRDRSYHFVGTAGDEELSVTPLVGLGKSSLLNKTIFHLMPCAEHKLTICTPYFNLPAVLVRNIIQLLRDGKQVEIIVGDKTANDFYIPEDQPFKIIGALPYLYEINLRRFLSRLQYYVNTDQLIVRLWKDDDNSYHLKGMWVDDEWMLLTGNNLNPRAWRLDLENAILIHDPKRQLGAMREKELKLIRTHTTVVKHYRDLQSIADYPVKVRKLIRRLRRIRIDRLISRIL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

5
  • GO:0032049 The chemical reactions and pathways resulting in the formation of cardiolipin, 1,3-bis(3-phosphatidyl)glycerol.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0008444 Catalysis of the reaction: sn-glycerol 3-phosphate + CDP-diacylglycerol = 3-(3-sn-phosphatidyl)-sn-glycerol 1-phosphate + CMP + H+.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0003882 Catalysis of the reaction: CDP-diacylglycerol + L-serine = CMP + O-sn-phosphatidyl-L-serine.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
19 447 Gene3D G3DSA:3.30.870.10 Endonuclease Chain A
238 431 CDD cd09136 PLDc_PSS_G_neg_2
9 215 SUPERFAMILY SSF56024 Phospholipase D/nuclease
352 379 ProSiteProfiles PS50035 Phospholipase D phosphodiesterase active site profile.
352 379 InterPro IPR001736 Phospholipase D/Transphosphatidylase
1 451 PIRSF PIRSF000850 PLD_PSS
24 230 FunFam G3DSA:3.30.870.10:FF:000008 CDP-diacylglycerol--serine O-phosphatidyltransferase
257 394 Pfam PF13091 PLD-like domain
257 394 InterPro IPR025202 Phospholipase D-like domain
253 393 SUPERFAMILY SSF56024 Phospholipase D/nuclease
231 447 FunFam G3DSA:3.30.870.10:FF:000006 CDP-diacylglycerol--serine O-phosphatidyltransferase
17 190 CDD cd09134 PLDc_PSS_G_neg_1
24 232 Gene3D G3DSA:3.30.870.10 Endonuclease Chain A
133 159 SMART SM00155 pld_4
133 159 InterPro IPR001736 Phospholipase D/Transphosphatidylase
352 379 SMART SM00155 pld_4
7 435 PANTHER PTHR12586 CDP-DIACYLGLYCEROL--SERINE O-PHOSPHATIDYLTRANSFERASE
7 435 InterPro IPR016270 CDP-alcohol phosphatidyltransferase class-II family

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
0.92
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Surrounding area
Pocket 2 P2Rank #2
0.194
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Surrounding area
Pocket 3 P2Rank #3
0.147
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Surrounding area
Pocket 4 P2Rank #4
0.02
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Surrounding area
Pocket 5 P2Rank #5
0.008
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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 #12
0.221
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Surrounding area
Pocket 2 FPocket #8
0.218
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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_A0A0H3GTV1
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4593
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GTV1

Pathways

KEGG R01800 BioCyc PHOSPHASERSYN-RXN