Protein target profile

KP13_05339

Aconitate hydratase 1

Genome: KpKP13 Gene: acnA AHE44986.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GRP5

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Length 890

Pocket druggability 0.824

Direct ligand evidence 0 25 total records

Functional annotation 0 EC 0 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

Independent pocket support: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 0.82, P2Rank 0.79). Use the 3D pocket comparison to verify whether they identify the same site. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.82. This is a computational pocket signal, not binding validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.79. 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 (%): 53.125 Lower values reduce human off-target concern.
Human E-value: 0.0
Gut microbiome similarity: 9.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 62.946 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: 94.0 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 0.824

Structure A0A0H3GRP5

Pocket Pocket 23

P2Rank 0.787

Structure A0A0H3GRP5

Pocket Pocket 1

ColabFold model

FPocket 0.772 · Pocket 21

P2Rank 0.827 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 451 / 4744 genomes with a hit

Prevalence 9.5%

Cross-references

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

Sequence

UniProt A0A0H3GRP5

Sequence

Primary amino-acid sequence viewer.

MSSTLREASKDTLQVNEKTWHYYSLPLAEKQLGEISRLPKSLKVLMENLLRWQDGDSVTEEDIRALAGWLQQAHADREIAYRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTAKVNPLSPVDLVIDHSVTVDRFGDDEAFEDNVRLEMERNHERYAFLRWGQQAFSRFSVVPPGTGICHQVNLEYLGRAVWSEEVNGQWMAWPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPDVVGFKLSGKLREGITATDLVLTVTQMLRQHGVVGKFVEFYGDGLDTLPLADRATIANMAPEYGATCGFFPIDDVTLSYMRLSGRSEEQVALVEAYAKAQGMWRQPGDEPVFTSTLALDMSSVEASLAGPKRPQDRVALGDVPKAFAASGELEVNHLQRQRQPVDYTLNGHHYSLPDGAVAIAAITSCTNTSNPSVLMAAGLLAKKAVERGLQPQPWVKASLAPGSKVVSDYLAHAGLTPYLDQLGFNLVGYGCTTCIGNSGPLPEPIEEAIKKGDLTVGAVLSGNRNFEGRIHPLVKTNWLASPPLVVAYALAGNMNIDLTREPLGQGKNGEPVYLKDIWPSGEEIARAVEQVSTEMFRKEYAEVFSGTEEWKAIKVEASDTYDWQEDSTYIRLSPFFDEMGVEPLPVEDIRGARILAMLGDSVTTDHISPAGSIKADSPAGRYLQEHGVARRDFNSYGSRRGNHEVMMRGTFANIRIRNEMVPGVEGGMTRHLPDPEPMAIYDAAMLYKAEGTPLAVIAGKEYGSGSSRDWAAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLRLTGEERIDISNLQSLQPGATVPVTLTRADGSQDAIPCRCRIDTATELTYYRNDGILHYVIRNML

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

No GO or EC annotations are currently loaded for this protein.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

46 records

Show feature table

Start	End	DB	Term	Name
653	890	FunFam	G3DSA:3.20.19.10:FF:000001	Aconitate hydratase
493	506	ProSitePatterns	PS01244	Aconitase family signature 2.
493	506	InterPro	IPR018136	Aconitase family, 4Fe-4S cluster binding site
630	889	SUPERFAMILY	SSF52016	LeuD/IlvD-like
10	625	SUPERFAMILY	SSF53732	Aconitase iron-sulfur domain
10	625	InterPro	IPR036008	Aconitase, iron-sulfur domain
691	818	Pfam	PF00694	Aconitase C-terminal domain
691	818	InterPro	IPR000573	Aconitase A/isopropylmalate dehydratase small subunit, swivel domain
592	650	Gene3D	G3DSA:6.10.190.10	-
14	889	PANTHER	PTHR11670	ACONITASE/IRON-RESPONSIVE ELEMENT FAMILY MEMBER
14	889	InterPro	IPR006249	Aconitase/Iron-responsive element-binding protein 2
653	890	Gene3D	G3DSA:3.20.19.10	Aconitase, domain 4
653	890	InterPro	IPR015928	Aconitase/3-isopropylmalate dehydratase, swivel
373	590	Gene3D	G3DSA:3.30.499.10	Aconitase, domain 3
373	590	InterPro	IPR015931	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3
85	564	CDD	cd01586	AcnA_IRP
6	372	Gene3D	G3DSA:3.30.499.10	Aconitase, domain 3
6	372	InterPro	IPR015931	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3
373	590	FunFam	G3DSA:3.30.499.10:FF:000009	Aconitate hydratase
5	372	FunFam	G3DSA:3.30.499.10:FF:000002	Aconitate hydratase
18	890	NCBIfam	TIGR01341	aconitate hydratase AcnA
18	890	InterPro	IPR006249	Aconitase/Iron-responsive element-binding protein 2
69	562	Pfam	PF00330	Aconitase family (aconitate hydratase)
69	562	InterPro	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
217	232	PRINTS	PR00415	Aconitase family signature
217	232	InterPro	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
431	442	PRINTS	PR00415	Aconitase family signature
431	442	InterPro	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
203	216	PRINTS	PR00415	Aconitase family signature
203	216	InterPro	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
493	506	PRINTS	PR00415	Aconitase family signature
493	506	InterPro	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
279	292	PRINTS	PR00415	Aconitase family signature
279	292	InterPro	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
293	306	PRINTS	PR00415	Aconitase family signature
293	306	InterPro	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
170	178	PRINTS	PR00415	Aconitase family signature
170	178	InterPro	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
372	386	PRINTS	PR00415	Aconitase family signature
372	386	InterPro	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
146	159	PRINTS	PR00415	Aconitase family signature
146	159	InterPro	IPR001030	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
427	443	ProSitePatterns	PS00450	Aconitase family signature 1.
427	443	InterPro	IPR018136	Aconitase family, 4Fe-4S cluster binding site
667	836	CDD	cd01580	AcnA_IRP_Swivel
667	836	InterPro	IPR044137	Aconitase A, swivel domain

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 #23

0.824

Unusual size

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Surrounding area

Site 2 FPocket #26

0.698

Likely same site as P2Rank 4 0.5 Å 14 shared residues 93% 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

0.787

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Surrounding area

Site 2 P2Rank #2

0.548

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Surrounding area

Site 3 P2Rank #3

0.512

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Surrounding area

Site 4 P2Rank #4

0.417

Likely same site as FPocket 26 0.5 Å 14 shared residues 93% of smaller site

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Surrounding area

Site 5 P2Rank #5

0.365

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Surrounding area

Binding pockets · FPocket

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

Site 1 FPocket #21

0.772

Likely same site as P2Rank 5 0.9 Å 16 shared residues 100% of smaller site

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Surrounding area

Site 2 FPocket #49

0.439

Unusual size

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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

0.827

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Surrounding area

Site 2 P2Rank #2

0.759

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Surrounding area

Site 3 P2Rank #3

0.539

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Surrounding area

Site 4 P2Rank #4

0.499

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Surrounding area

Site 5 P2Rank #5

0.494

Likely same site as FPocket 21 0.9 Å 16 shared residues 100% of smaller site

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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_A0A0H3GRP5	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_05339	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.

25 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 14 similarity-based ZINC candidates

Best available ligand signal

ATH PDB via homolog 187.1 Da · LogP -5.48 · TPSA 140.6 Open detail RCSB PDB

F3S PDB via homolog Detail RCSB PDB

FLC PDB via homolog Detail RCSB PDB

ICT PDB via homolog Detail RCSB PDB

KP1 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
ATH RCSB PDB	1FGH	P20004	187.1 Da LogP -5.48 TPSA 140.6	✓ Ro5	✓ Clean	`C(=C(/[C@H](C(=O)[O-])O)\C(=O)[O-])/C(=O)[O-]`
F3S RCSB PDB	5ACN	P16276	295.8 Da LogP 2.59 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]2S[Fe]3[S]2[Fe]1S3`
FLC RCSB PDB	1B0K	P16276	189.1 Da LogP -5.25 TPSA 140.6	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O`
ICT RCSB PDB	1B0J	P16276	192.1 Da LogP -1.39 TPSA 132.1	✓ Ro5	✓ Clean	`C([C@@H]([C@H](C(=O)O)O)C(=O)O)C(=O)O`
KP1 RCSB PDB	4KP1	P81291	132.2 Da LogP 0.92 TPSA 40.5	✓ Ro5	✓ Clean	`CC(C)(CC(C)(C)O)O`
MIC RCSB PDB	1AMI	P20004	206.2 Da LogP -1.00 TPSA 132.1	✓ Ro5	✓ Clean	`C[C@@]([C@H](CC(=O)O)C(=O)O)(C(=O)O)O`
NIC RCSB PDB	8ACN	P20004	193.1 Da LogP -1.45 TPSA 138.0	✓ Ro5	✓ Clean	`C([C@@H]([C@H](C(=O)O)O)[N+](=O)[O-])C(=O)O`
NTC RCSB PDB	1NIS	P20004	193.1 Da LogP -1.45 TPSA 138.0	✓ Ro5	✓ Clean	`C(C(=O)O)[C@@](C[N+](=O)[O-])(C(=O)O)O`
O RCSB PDB	1B0K	P16276	18.0 Da LogP -0.82 TPSA 31.5	✓ Ro5	✓ Clean	`O`
TRA RCSB PDB	1ACO	P20004	171.1 Da LogP -4.45 TPSA 120.4	✓ Ro5	✓ Clean	`C(/C(=C\C(=O)[O-])/C(=O)[O-])C(=O)[O-]`
TRC RCSB PDB	5ACN	P16276	176.1 Da LogP -0.36 TPSA 111.9	✓ Ro5	✓ Clean	`C(C(CC(=O)O)C(=O)O)C(=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
ZINC1577651 ZINC	0.684	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@H](C(=O)O)[C@@H](CC(=O)O)C(=O)O`
ZINC1577652 ZINC	0.684	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@@H](C(=O)O)[C@@H](CC(=O)O)C(=O)O`
ZINC1577653 ZINC	0.684	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@H](C(=O)O)[C@H](CC(=O)O)C(=O)O`
ZINC1623550 ZINC	0.529	240.1 Da LogP 2.00 TPSA 40.5	✓ Ro5	✓ Clean	`CC(C)(O)CC(O)(C(F)(F)F)C(F)(F)F`
ZINC45068939 ZINC	0.519	252.2 Da LogP 1.14 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)C[C@H](CC(=O)c1ccc(O)cc1)C(=O)O`
ZINC45068942 ZINC	0.519	252.2 Da LogP 1.14 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)C[C@@H](CC(=O)c1ccc(O)cc1)C(=O)O`
ZINC168333116 ZINC	0.515	225.2 Da LogP 0.32 TPSA 100.7	✓ Ro5	✓ Clean	`O=C(O)[C@@H](O)[C@H](Cc1ccccc1)[N+](=O)[O-]`
ZINC168342027 ZINC	0.515	225.2 Da LogP 0.32 TPSA 100.7	✓ Ro5	✓ Clean	`O=C(O)[C@H](O)[C@H](Cc1ccccc1)[N+](=O)[O-]`
ZINC33992595 ZINC	0.515	225.2 Da LogP 0.32 TPSA 100.7	✓ Ro5	✓ Clean	`O=C(O)[C@@H](O)[C@@H](Cc1ccccc1)[N+](=O)[O-]`
ZINC34050089 ZINC	0.515	225.2 Da LogP 0.32 TPSA 100.7	✓ Ro5	✓ Clean	`O=C(O)[C@H](O)[C@@H](Cc1ccccc1)[N+](=O)[O-]`
ZINC1532902 ZINC	0.500	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106 ZINC	0.500	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC4212247 ZINC	0.500	292.1 Da LogP -1.16 TPSA 189.7	1 viol.	✓ Clean	`O=C(O)C[C@@H](C(=O)O)C(P(=O)(O)O)P(=O)(O)O`
ZINC5131772 ZINC	0.500	292.1 Da LogP -1.16 TPSA 189.7	1 viol.	✓ Clean	`O=C(O)C[C@H](C(=O)O)C(P(=O)(O)O)P(=O)(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.