KpATCC43816 Protein target profile

rieske [2Fe-2S] domain protein

Accession: VK055_4109

Gene: AIK82655.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GXI0

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Length 107

Pocket druggability (FPocket · AlphaFold DB model) 0.135

Direct ligand evidence 0 57 total records

Functional annotation 0 EC 2 GO

Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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

Main supporting evidence

Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 7 structural and 0 bioactivity records.

Risks to review

Human similarity Top human hit identity: 34.328%. Microbiome similarity 43 of 4744 screened genomes (0.9%) have a significant similarity hit. Mixed conservation Core/accessory calls are not fully concordant. Weak predicted binding pocket FPocket selected-pocket score 0.14.

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: Hit
Human identity (%): 34.328 Lower values reduce human off-target concern.
Human E-value: 2.22e-09
Gut microbiome similarity: 0.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 43.59 Higher values support similarity to known essential genes.
DEG E-value: 4.65e-15 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 93.89 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)

Structure A0A0H3GXI0

Pocket No pockets

Druggability (FPocket) 0.135

Structure A0A0H3GXI0

Pocket Pocket 2

ColabFold model

FPocket 0.046 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 43 / 4744 genomes with a hit

Prevalence 0.9%

Metabolic context

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

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSWIGVCDAEQVQEDFPYSGNIDGKEIGIYLIDGEYYALEDVCPHAYALLSQGFVEDGKVECPLHEAVFDVKTGQCLHGPGGRNLNRYPVRVYDNQIQITFIEENVA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

9 records

Show feature table

Start	End	DB	Term	Name
3	99	CDD	cd03528	Rieske_RO_ferredoxin
3	99	ProSiteProfiles	PS51296	Rieske [2Fe-2S] iron-sulfur domain profile.
3	99	InterPro	IPR017941	Rieske [2Fe-2S] iron-sulphur domain
2	89	Pfam	PF00355	Rieske [2Fe-2S] domain
2	89	InterPro	IPR017941	Rieske [2Fe-2S] iron-sulphur domain
1	101	Gene3D	G3DSA:2.102.10.10	-
1	101	InterPro	IPR036922	Rieske [2Fe-2S] iron-sulphur domain superfamily
3	101	PANTHER	PTHR21496	FERREDOXIN-RELATED
1	101	SUPERFAMILY	SSF50022	ISP 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.

Download VMD script Full viewer

No pockets are loaded yet for the displayed AlphaFold DB model AF_A0A0H3GXI0 structure. Run experimental pocket backfill to show FPocket/P2Rank overlays on this structure.

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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'.

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_A0A0H3GXI0	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_4109	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.

57 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 7 records from similar proteins

Structural ligands 7 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

9CA PDB via homolog 167.2 Da · LogP 3.32 · TPSA 15.8 Open detail RCSB PDB

9FL PDB via homolog Detail RCSB PDB

BPY PDB via homolog Detail RCSB PDB

FES PDB via homolog Detail RCSB PDB

H2S 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
9CA RCSB PDB	2DE7	Q8GI16	167.2 Da LogP 3.32 TPSA 15.8	✓ Ro5	✓ Clean	`c1ccc2c(c1)c3ccccc3[nH]2`
9FL RCSB PDB	4NBE	Q8GI16	166.2 Da LogP 3.26 TPSA 0.0	✓ Ro5	✓ Clean	`c1ccc-2c(c1)Cc3c2cccc3`
BPY RCSB PDB	6LLH	Q8GI16	186.2 Da LogP 2.76 TPSA 40.5	✓ Ro5	Alert	`c1ccc(cc1)c2cccc(c2O)O`
FES RCSB PDB	2I7F	A2TC31	175.8 Da LogP 1.29 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]S[Fe]1`
H2S RCSB PDB	1VCK	Q8GI16	34.1 Da LogP 0.11 TPSA 0.0	✓ Ro5	✓ Clean	`S`
OXY RCSB PDB	3VMH	Q8GI16	32.0 Da LogP 0.07 TPSA 34.1	✓ Ro5	✓ Clean	`O=O`
WBP RCSB PDB	6LLF	Q8GI16	202.2 Da LogP 2.47 TPSA 60.7	✓ Ro5	Alert	`c1ccc(c(c1)c2cccc(c2O)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
ZINC6091722 ZINC	0.824	218.2 Da LogP 2.18 TPSA 80.9	✓ Ro5	Alert	`Oc1cccc(-c2cccc(O)c2O)c1O`
ZINC1841232 ZINC	0.800	246.3 Da LogP 4.73 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1c(-c2ccccc2)cccc1-c1ccccc1`
ZINC1671067 ZINC	0.778	256.3 Da LogP 4.96 TPSA 31.6	✓ Ro5	✓ Clean	`c1ccc2c(c1)[nH]c1cc3c(cc12)[nH]c1ccccc13`
ZINC59200446 ZINC	0.778	254.3 Da LogP 4.83 TPSA 0.0	✓ Ro5	✓ Clean	`c1ccc2c(c1)Cc1cc3c(cc1-2)Cc1ccccc1-3`
ZINC16697844 ZINC	0.737	256.3 Da LogP 4.96 TPSA 31.6	✓ Ro5	✓ Clean	`c1ccc2c(c1)[nH]c1cc3[nH]c4ccccc4c3cc12`
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`
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`
ZINC34543519 ZINC	0.684	256.3 Da LogP 4.96 TPSA 31.6	✓ Ro5	✓ Clean	`c1ccc2c(c1)[nH]c1ccc3[nH]c4ccccc4c3c12`
ZINC3877568 ZINC	0.684	211.3 Da LogP 4.05 TPSA 15.8	✓ Ro5	✓ Clean	`S=c1c2ccccc2[nH]c2ccccc12`
ZINC4667598 ZINC	0.684	208.3 Da LogP 3.02 TPSA 17.1	✓ Ro5	✓ Clean	`O=C1Cc2ccccc2-c2ccccc2C1`
ZINC6745008 ZINC	0.684	256.3 Da LogP 4.96 TPSA 31.6	✓ Ro5	✓ Clean	`c1ccc2c(c1)[nH]c1c2ccc2c3ccccc3[nH]c21`
ZINC77291353 ZINC	0.684	223.2 Da LogP 2.04 TPSA 49.9	✓ Ro5	✓ Clean	`O=c1c(=O)c2ccccc2[nH]c2ccccc12`
ZINC78200974 ZINC	0.684	210.3 Da LogP 3.36 TPSA 0.0	✓ Ro5	Alert	`S=C1c2ccccc2Cc2ccccc21`
ZINC1712294 ZINC	0.667	204.3 Da LogP 3.71 TPSA 0.0	✓ Ro5	✓ Clean	`c1ccc2c(c1)CC1=C2Cc2ccccc21`
ZINC78762652 ZINC	0.667	206.2 Da LogP 3.80 TPSA 31.6	✓ Ro5	✓ Clean	`c1ccc2c(c1)[nH]c1c3ccccc3[nH]c21`
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`
ZINC113917747 ZINC	0.650	208.3 Da LogP 3.02 TPSA 17.1	✓ Ro5	✓ Clean	`O=C1Cc2ccccc2Cc2ccccc21`
ZINC157625 ZINC	0.650	211.3 Da LogP 4.05 TPSA 15.8	✓ Ro5	✓ Clean	`S=c1[nH]c2ccccc2c2ccccc12`
ZINC1641025 ZINC	0.640	204.7 Da LogP 3.71 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1c(Cl)cccc1-c1ccccc1`
ZINC34086259 ZINC	0.640	249.1 Da LogP 3.82 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1c(Br)cccc1-c1ccccc1`
ZINC1570220 ZINC	0.636	216.3 Da LogP 4.41 TPSA 0.0	✓ Ro5	✓ Clean	`c1ccc2c(c1)Cc1cc3ccccc3cc1-2`
ZINC1689792 ZINC	0.636	217.3 Da LogP 4.47 TPSA 15.8	✓ Ro5	✓ Clean	`c1ccc2cc3c(cc2c1)[nH]c1ccccc13`
ZINC1709155 ZINC	0.632	236.3 Da LogP 2.85 TPSA 34.1	✓ Ro5	✓ Clean	`O=C1Cc2ccccc2C(=O)Cc2ccccc21`
ZINC14686440 ZINC	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442 ZINC	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…`
ZINC14686444 ZINC	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…`
ZINC71256729 ZINC	0.625	220.3 Da LogP 4.21 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1cccc2c(-c3ccccc3)cccc12`
ZINC1038911 ZINC	0.609	245.1 Da LogP 4.02 TPSA 0.0	✓ Ro5	✓ Clean	`Brc1ccc2c(c1)Cc1ccccc1-2`
ZINC1464806 ZINC	0.609	292.1 Da LogP 3.86 TPSA 0.0	✓ Ro5	✓ Clean	`Ic1ccc2c(c1)Cc1ccccc1-2`
ZINC146559825 ZINC	0.609	325.0 Da LogP 4.85 TPSA 15.8	✓ Ro5	✓ Clean	`Brc1cc2[nH]c3ccccc3c2cc1Br`
ZINC160335 ZINC	0.609	246.1 Da LogP 4.08 TPSA 15.8	✓ Ro5	✓ Clean	`Brc1ccc2[nH]c3ccccc3c2c1`
ZINC1632626 ZINC	0.609	200.7 Da LogP 3.91 TPSA 0.0	✓ Ro5	✓ Clean	`Clc1ccc2c(c1)Cc1ccccc1-2`
ZINC2023096 ZINC	0.609	201.7 Da LogP 3.97 TPSA 15.8	✓ Ro5	✓ Clean	`Clc1ccc2[nH]c3ccccc3c2c1`
ZINC2070660 ZINC	0.609	293.1 Da LogP 3.93 TPSA 15.8	✓ Ro5	✓ Clean	`Ic1ccc2c(c1)[nH]c1ccccc12`
ZINC3137092 ZINC	0.609	293.1 Da LogP 3.93 TPSA 15.8	✓ Ro5	✓ Clean	`Ic1ccc2[nH]c3ccccc3c2c1`
ZINC35323422 ZINC	0.609	246.1 Da LogP 4.08 TPSA 15.8	✓ Ro5	✓ Clean	`Brc1ccc2c(c1)[nH]c1ccccc12`
ZINC3847493 ZINC	0.609	201.7 Da LogP 3.97 TPSA 15.8	✓ Ro5	✓ Clean	`Clc1ccc2c(c1)[nH]c1ccccc12`
ZINC55351995 ZINC	0.609	245.1 Da LogP 4.02 TPSA 0.0	✓ Ro5	✓ Clean	`Brc1ccc2c(c1)-c1ccccc1C2`
ZINC18279994 ZINC	0.600	264.3 Da LogP 3.73 TPSA 72.0	✓ Ro5	✓ Clean	`Oc1c(-c2[nH]c3ccccc3c2O)[nH]c2ccccc12`
ZINC394382 ZINC	0.593	214.2 Da LogP 2.76 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1cccc(-c2ccccc2)c1O`
ZINC1712464 ZINC	0.591	262.3 Da LogP 4.43 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1cc(-c2ccccc2)c(O)cc1-c1ccccc1`
ZINC4805074 ZINC	0.591	223.3 Da LogP 3.28 TPSA 32.6	✓ Ro5	✓ Clean	`ON=C1Cc2ccccc2-c2ccccc2C1`
ZINC116811035 ZINC	0.583	242.3 Da LogP 4.92 TPSA 0.0	✓ Ro5	✓ Clean	`c1ccc(-c2ccc3c(c2)Cc2ccccc2-3)cc1`
ZINC13490703 ZINC	0.583	256.3 Da LogP 4.96 TPSA 31.6	✓ Ro5	✓ Clean	`c1ccc2c(c1)[nH]c1c2ccc2[nH]c3ccccc3c21`
ZINC34071153 ZINC	0.583	243.3 Da LogP 4.99 TPSA 15.8	✓ Ro5	✓ Clean	`c1ccc(-c2ccc3[nH]c4ccccc4c3c2)cc1`
ZINC53312883 ZINC	0.583	243.3 Da LogP 4.99 TPSA 15.8	✓ Ro5	✓ Clean	`c1ccc(-c2ccc3c(c2)[nH]c2ccccc23)cc1`
ZINC71785795 ZINC	0.579	208.3 Da LogP 4.23 TPSA 0.0	✓ Ro5	✓ Clean	`c1ccc2c(c1)CCCCc1ccccc1-2`
ZINC71785798 ZINC	0.579	206.3 Da LogP 4.01 TPSA 0.0	✓ Ro5	✓ Clean	`C1=CCc2ccccc2-c2ccccc2C1`
ZINC13398039 ZINC	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@](O)(CC(=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 A0A0H3GXI0