Protein target profile

KP13_31485

Malonyl CoA-acyl carrier protein transacylase

Genome: KpKP13 Gene: AHE45280.1 fabD 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GR66

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Length 309

Pocket druggability 0.658

Direct ligand evidence 0 61 total records

Functional annotation 1 EC 4 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

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Moderate predicted binding pocket FPocket selected-pocket score 0.66. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.84. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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 (%): 34.333 Lower values reduce human off-target concern.
Human E-value: 1.25e-41
Gut microbiome similarity: 7.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 90.584 Higher values support similarity to known essential genes.
DEG E-value: 0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 97.8 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 0.658

Structure A0A0H3GR66

Pocket Pocket 7

P2Rank 0.84

Structure A0A0H3GR66

Pocket Pocket 1

ColabFold model

FPocket 0.613 · Pocket 1

P2Rank 0.845 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 334 / 4744 genomes with a hit

Prevalence 7.0%

Cross-references

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

Sequence

UniProt A0A0H3GR66

Sequence

Primary amino-acid sequence viewer.

MTQFAFVFPGQGSQAVGMLAEMAAAWPVIEETFGEASAALGYDLWALTQQGPAEELNKTWQTQPALLAASVALYRVWQQQGGKAPTLLAGHSLGEYSALVCAGVIGFADAVRLVELRGKFMQEAVPEGTGAMSAIIGLDDAAIAKACEESAEGQVVSPVNYNSPGQVVIAGHKEAVERAGAACKAAGAKRALPLPVSVPSHCALMKPAAEKLAVELQKITFNAPTIPVVNNVDVKCETAPDAIRDALVRQLYSPVQWTKTVEFMAAEGVSHLYEVGPGKVLTGLTKRIVDTLTASALNEPAAMSAALEQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

2.3.1.39

Gene Ontology (GO)

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:0004314 Catalysis of the reaction: malonyl-CoA + [acyl-carrier protein] = CoA + malonyl-[acyl-carrier protein].
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0006633 The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

17 records

Show feature table

Start	End	DB	Term	Name
125	197	Gene3D	G3DSA:3.30.70.250	-
6	282	Pfam	PF00698	Acyl transferase domain
6	282	InterPro	IPR014043	Acyl transferase
128	197	SUPERFAMILY	SSF55048	Probable ACP-binding domain of malonyl-CoA ACP transacylase
128	197	InterPro	IPR016036	Malonyl-CoA ACP transacylase, ACP-binding
6	286	Gene3D	G3DSA:3.40.366.10	-
6	286	InterPro	IPR001227	Acyl transferase domain superfamily
3	298	PANTHER	PTHR42681	MALONYL-COA-ACYL CARRIER PROTEIN TRANSACYLASE, MITOCHONDRIAL
4	307	SUPERFAMILY	SSF52151	FabD/lysophospholipase-like
4	307	InterPro	IPR016035	Acyl transferase/acyl hydrolase/lysophospholipase
3	291	NCBIfam	TIGR00128	ACP S-malonyltransferase
3	291	InterPro	IPR004410	Malonyl CoA-acyl carrier protein transacylase, FabD-type
1	309	PIRSF	PIRSF000446	Mct
1	309	InterPro	IPR024925	Malonyl CoA-acyl carrier protein transacylase
7	308	SMART	SM00827	Acyl transferase domain in polyketide synthase (PKS) enzymes.
7	308	InterPro	IPR014043	Acyl transferase
125	197	FunFam	G3DSA:3.30.70.250:FF:000001	Malonyl CoA-acyl carrier protein transacylase

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 #7

0.658

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Surrounding area

Site 2 FPocket #2

0.314

Likely same site as P2Rank 1 4.2 Å 10 shared residues 71% of smaller site

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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1

0.84

Likely same site as FPocket 2 4.2 Å 10 shared residues 71% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.04

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Surrounding area

Site 3 P2Rank #3

0.004

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Surrounding area

Residue sets

UniProt: Active site:201-201

UniProt: Active site:92-92

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_A0A0H3GR66	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_31485	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.

61 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 11 records from similar proteins

Structural ligands 11 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

8JZ PDB via homolog 116.2 Da · LogP 1.35 · TPSA 26.3 Open detail RCSB PDB

9EF PDB via homolog Detail RCSB PDB

AE3 PDB via homolog Detail RCSB PDB

AE4 PDB via homolog Detail RCSB PDB

COZ 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
8JZ RCSB PDB	3HJV	Q9KQH6	116.2 Da LogP 1.35 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCOC(=O)C`
9EF RCSB PDB	6U0J	P0AAI9	383.3 Da LogP -1.76 TPSA 174.3	1 viol.	✓ Clean	`CC(=O)NCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)…`
AE3 RCSB PDB	2C2N	Q8IVS2	134.2 Da LogP 0.03 TPSA 38.7	✓ Ro5	✓ Clean	`CCOCCOCCO`
AE4 RCSB PDB	2C2N	Q8IVS2	266.3 Da LogP 0.08 TPSA 66.4	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCO`
COZ RCSB PDB	2G2Z	P0AAI9	767.5 Da LogP -1.67 TPSA 346.6	3 viol.	✓ Clean	`CC(C)(CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([…`
CXS RCSB PDB	3HJV	Q9KQH6	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`C1CCC(CC1)NCCCS(=O)(=O)O`
DXE RCSB PDB	2C2N	Q8IVS2	90.1 Da LogP 0.28 TPSA 18.5	✓ Ro5	✓ Clean	`COCCOC`
E5U RCSB PDB	6L3M	Q8KUH4	134.1 Da LogP -0.83 TPSA 83.8	✓ Ro5	✓ Clean	`COC(C(=O)O)C(=O)O`
MLA RCSB PDB	2G2Z	P0AAI9	104.1 Da LogP -0.45 TPSA 74.6	✓ Ro5	✓ Clean	`C(C(=O)O)C(=O)O`
MLI RCSB PDB	2G2Y	P0AAI9	102.0 Da LogP -3.12 TPSA 80.3	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(=O)[O-]`
NHE RCSB PDB	3R97	Q5H4I7	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`C1CCC(CC1)NCCS(=O)(=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
ZINC12501520 ZINC	1.000	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1710230 ZINC	1.000	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC1CCCCC1`
ZINC3874716 ZINC	1.000	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769 ZINC	1.000	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548 ZINC	1.000	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829 ZINC	1.000	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830 ZINC	1.000	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1677799 ZINC	0.810	200.3 Da LogP 3.69 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCCCCOC(C)=O`
ZINC1694423 ZINC	0.810	228.4 Da LogP 4.47 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOC(C)=O`
ZINC1848558 ZINC	0.810	214.3 Da LogP 4.08 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCOC(C)=O`
ZINC59725169 ZINC	0.810	242.4 Da LogP 4.86 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCOC(C)=O`
ZINC2004372 ZINC	0.786	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC1CCCCC1`
ZINC38364153 ZINC	0.786	235.3 Da LogP 1.58 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC1CCCCC1`
ZINC1680748 ZINC	0.739	204.3 Da LogP 1.38 TPSA 44.8	✓ Ro5	✓ Clean	`CCCCOCCOCCOC(C)=O`
ZINC15146151 ZINC	0.700	286.4 Da LogP 4.01 TPSA 52.6	✓ Ro5	✓ Clean	`CC(=O)OCCCCCCCCCCCCOC(C)=O`
ZINC1532902 ZINC	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC1684744 ZINC	0.700	244.3 Da LogP 2.84 TPSA 52.6	✓ Ro5	✓ Clean	`CC(=O)OCCCCCCCCCOC(C)=O`
ZINC1694794 ZINC	0.700	202.2 Da LogP 1.67 TPSA 52.6	✓ Ro5	✓ Clean	`CC(=O)OCCCCCCOC(C)=O`
ZINC2018106 ZINC	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC2386050 ZINC	0.700	230.3 Da LogP 2.45 TPSA 52.6	✓ Ro5	✓ Clean	`CC(=O)OCCCCCCCCOC(C)=O`
ZINC2556930 ZINC	0.700	216.3 Da LogP 2.06 TPSA 52.6	✓ Ro5	✓ Clean	`CC(=O)OCCCCCCCOC(C)=O`
ZINC5161313 ZINC	0.700	258.4 Da LogP 3.23 TPSA 52.6	✓ Ro5	✓ Clean	`CC(=O)OCCCCCCCCCCOC(C)=O`
ZINC115086873 ZINC	0.688	209.2 Da LogP -1.08 TPSA 83.2	✓ Ro5	✓ Clean	`NOCCOCCOCCOCCO`
ZINC137432264 ZINC	0.688	457.6 Da LogP -0.91 TPSA 129.3	1 viol.	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC146143823 ZINC	0.688	237.3 Da LogP -1.00 TPSA 83.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCO`
ZINC1542984442 ZINC	0.688	413.5 Da LogP -0.93 TPSA 120.1	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1565503710 ZINC	0.688	254.3 Da LogP -0.03 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCS`
ZINC1580161 ZINC	0.688	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118 ZINC	0.688	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257 ZINC	0.688	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1857792028 ZINC	0.688	430.6 Da LogP 0.04 TPSA 94.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC230494776 ZINC	0.688	325.4 Da LogP -0.96 TPSA 101.6	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654 ZINC	0.688	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC38917157 ZINC	0.688	210.3 Da LogP -0.04 TPSA 47.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCS`
ZINC44076059 ZINC	0.688	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101 ZINC	0.688	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5650743 ZINC	0.688	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC5997860 ZINC	0.688	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC6403917 ZINC	0.688	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC77271182 ZINC	0.688	281.3 Da LogP -0.98 TPSA 92.4	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCO`
ZINC83253921 ZINC	0.688	369.5 Da LogP -0.95 TPSA 110.9	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC90741446 ZINC	0.688	386.5 Da LogP 0.02 TPSA 84.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC90741447 ZINC	0.688	298.4 Da LogP -0.01 TPSA 66.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCS`
ZINC1586759 ZINC	0.667	202.2 Da LogP 1.67 TPSA 52.6	✓ Ro5	✓ Clean	`CCCCOC(=O)C(=O)OCCCC`
ZINC3593496 ZINC	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497 ZINC	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC144169243 ZINC	0.647	281.3 Da LogP -1.37 TPSA 89.4	✓ Ro5	✓ Clean	`OCCOCCOCCNCCOCCOCCO`
ZINC205758716 ZINC	0.647	457.6 Da LogP -1.31 TPSA 126.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCNCCOCCOCCOCCOCCO`
ZINC575441396 ZINC	0.647	369.5 Da LogP -1.34 TPSA 107.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCNCCOCCOCCOCCO`
ZINC43068418 ZINC	0.630	240.4 Da LogP 4.64 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCOC(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.