KpATCC43816 Protein target profile

putative transcriptional accessory protein

Accession: VK055_3694

Gene: AIK82249.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GYF8

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Length 776

Pocket druggability (P2Rank · AlphaFold DB model) 0.803

Direct ligand evidence 0 39 total records

Functional annotation 0 EC 6 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

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.80. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 1 structural and 2 bioactivity records.

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: Hit
Human identity (%): 37.931 Lower values reduce human off-target concern.
Human E-value: 9.04e-07
Gut microbiome similarity: 6.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 71.632 Higher values support similarity to known essential genes.
DEG E-value: 0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 89.2 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) 0.803

Structure A0A0H3GYF8

Pocket Pocket 1

Druggability (FPocket) 0.251

Structure A0A0H3GYF8

Pocket Pocket 36

ColabFold model

P2Rank 0.9 · Pocket 1

FPocket 0.55 · Pocket 4

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 293 / 4744 genomes with a hit

Prevalence 6.2%

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.

MMNDSLCRIIAGELQARAEQVEAAVRLLDEGNTVPFIARYRKEVTGGLDDTQLRNLETRLGYLRELEDRRQAILKSIAEQGKLTDALEKAINTTLSKTELEDLYLPYKPKRRTRGQIAIEAGLEPLADLLWNEPAHDPEAEAAKYIDADKGVADSKAALDGARYILMERFAEDAALLAKVRDYLWKNAHLVSTVVSGKEEEGAKFRDYFDHHEPIATVPSHRALAMFRGRNEGVLQLSLNADPQFDEPPKESHGEQIIIDHLGLRLNNAPADSWRKGVVSWTWRIKVLMHLETELMGTVRERAEDEAINVFARNLHDLLMAAPAGLRATMGLDPGLRTGVKVAVVDATGKLVATDTIYPHTGQAAKAAVAVAALCEKYNVELVAIGNGTASRETERFFLDVQKQFPKVTAQKVIVSEAGASVYSASELAAQEFPDLDVSLRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVSQTQLARKLDAVVEDCVNAVGVDLNTASVPLLTRVAGLTRMMAQNIVAWRDENGQFQNRQQLLKVSRLGPKAFEQCAGFLRINHGDNPLDASTVHPEAYPVVERILAATQQALKDLMGNSSALRHLKAVDFTDEKFGVPTVTDIIKELEKPGRDPRPEFKTAKFADGVETMNDLLPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSDRFVEDPHTVVKAGDIVKVKVMEVDLPRKRIALTMRLDEQPGDSNARRGGGQERPQGNRPAAKAAKPRGREAQPAGNSAMMDALAAAMGKKR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

GO:0006139 Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
GO:0003676 Binding to a nucleic acid.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0003729 Binding to messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
GO:0003735 The action of a molecule that contributes to the structural integrity of the ribosome.
GO:0006412 The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

41 records

Show feature table

Start	End	DB	Term	Name
634	724	FunFam	G3DSA:2.40.50.140:FF:000051	RNA-binding transcriptional accessory protein
499	630	Gene3D	G3DSA:1.10.150.310	-
649	720	SMART	SM00316	S1_6
649	720	InterPro	IPR022967	RNA-binding domain, S1
720	776	MobiDBLite	mobidb-lite	consensus disorder prediction
2	322	SUPERFAMILY	SSF158832	Tex N-terminal region-like
323	469	SUPERFAMILY	SSF53098	Ribonuclease H-like
323	469	InterPro	IPR012337	Ribonuclease H-like superfamily
111	328	FunFam	G3DSA:1.10.3500.10:FF:000002	RNA-binding transcriptional accessory protein
638	722	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
638	722	InterPro	IPR012340	Nucleic acid-binding, OB-fold
10	193	Pfam	PF09371	Tex-like protein N-terminal domain
10	193	InterPro	IPR018974	Tex-like protein, N-terminal
560	632	SUPERFAMILY	SSF47781	RuvA domain 2-like
560	632	InterPro	IPR010994	RuvA domain 2-like
631	724	Gene3D	G3DSA:2.40.50.140	-
631	724	InterPro	IPR012340	Nucleic acid-binding, OB-fold
499	630	FunFam	G3DSA:1.10.150.310:FF:000001	RNA-binding transcriptional accessory protein
328	451	Pfam	PF16921	Tex protein YqgF-like domain
328	451	InterPro	IPR032639	Tex protein, YqgF-like domain
470	558	SUPERFAMILY	SSF47781	RuvA domain 2-like
470	558	InterPro	IPR010994	RuvA domain 2-like
651	720	Pfam	PF00575	S1 RNA binding domain
651	720	InterPro	IPR003029	S1 domain
111	498	Gene3D	G3DSA:1.10.3500.10	-
111	498	InterPro	IPR023323	Tex-like domain superfamily
326	451	FunFam	G3DSA:3.30.420.140:FF:000001	RNA-binding transcriptional accessory protein
3	110	Gene3D	G3DSA:1.10.10.650	-
3	110	InterPro	IPR023319	Tex-like protein, HTH domain superfamily
326	451	Gene3D	G3DSA:3.30.420.140	-
326	451	InterPro	IPR037027	YqgF/RNase H-like domain superfamily
651	720	ProSiteProfiles	PS50126	S1 domain profile.
651	718	CDD	cd05685	S1_Tex
651	718	InterPro	IPR044146	Tex, S1 domain
561	630	Pfam	PF17674	HHH domain
561	630	InterPro	IPR041692	HHH domain 9
39	744	PANTHER	PTHR10724	30S RIBOSOMAL PROTEIN S1
491	555	Pfam	PF12836	Helix-hairpin-helix motif
327	424	SMART	SM00732	rnase_8s
327	424	InterPro	IPR006641	YqgF/RNase H-like domain
2	110	FunFam	G3DSA:1.10.10.650:FF:000001	S1 RNA-binding domain 1

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

0.803

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Surrounding area

Pocket 2 P2Rank #2

0.443

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Surrounding area

Pocket 3 P2Rank #3

0.162

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Surrounding area

Pocket 4 P2Rank #4

0.143

Likely same site as FPocket 36 5.7 Å 11 shared residues 100% of smaller site

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Surrounding area

Pocket 5 P2Rank #5

0.054

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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 #36

0.251 Unusual size

Likely same site as P2Rank 4 5.7 Å 11 shared residues 100% of smaller site

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Surrounding area

Binding pockets · P2Rank

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

Pocket 1 P2Rank #1

0.9

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Surrounding area

Pocket 2 P2Rank #2

0.453

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Surrounding area

Pocket 3 P2Rank #3

0.324

Likely same site as FPocket 4 1.1 Å 11 shared residues 92% of smaller site

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Surrounding area

Pocket 4 P2Rank #4

0.254

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Surrounding area

Pocket 5 P2Rank #5

0.194

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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 #4

0.55

Likely same site as P2Rank 3 1.1 Å 11 shared residues 92% of smaller site

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Surrounding area

Pocket 2 FPocket #2

0.215

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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_A0A0H3GYF8	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_3694	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.

39 records

Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records

Transferred evidence 3 records from similar proteins

Structural ligands 1 0 loaded crystals

Measured bioactivity 2 direct and transferred ChEMBL records

Proposed compounds 36 similarity-based ZINC candidates

Best available ligand signal

VGL PDB via homolog 124.1 Da · LogP 0.17 · TPSA 63.1 Open detail RCSB PDB

DXH ChEMBL via homolog · pchembl 7.47 (~33.9 nM) Detail ChEMBL

DWT ChEMBL via homolog · pchembl 7.14 (~72.4 nM) Detail ChEMBL

ZINC20357720 ZINC proposed compound · Tanimoto 0.581 Detail ZINC

ZINC2749775 ZINC proposed compound · Tanimoto 0.552 Detail ZINC

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
VGL RCSB PDB	4NNI	P9WH43	124.1 Da LogP 0.17 TPSA 63.1	✓ Ro5	✓ Clean	`c1cnc(cn1)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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
DXH ChEMBL	Q14690	7.47 ~33.9 nM	503.5 Da LogP 5.75 TPSA 97.6	2 viol.	✓ Clean	`Cc1ccc(cc1Nc2c3cnn(c3nc(n2)c4cccnc4)C)C(=O)Nc5c…`
DWT ChEMBL	Q14690	7.14 ~72.4 nM	503.5 Da LogP 5.75 TPSA 97.6	2 viol.	✓ Clean	`Cc1ccc(cc1Nc2c3cn(nc3nc(n2)c4cccnc4)C)C(=O)Nc5c…`

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
ZINC20357720 ZINC	0.581	228.2 Da LogP 1.41 TPSA 80.1	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)c1cnccn1`
ZINC2749775 ZINC	0.552	272.3 Da LogP -0.57 TPSA 109.8	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)c1cnccn1)c1cnccn1`
ZINC20496347 ZINC	0.548	219.3 Da LogP 1.88 TPSA 46.1	✓ Ro5	✓ Clean	`O=C(c1cnccn1)N1CCCCCCC1`
ZINC5705248 ZINC	0.548	205.3 Da LogP 1.49 TPSA 46.1	✓ Ro5	✓ Clean	`O=C(c1cnccn1)N1CCCCCC1`
ZINC69048726 ZINC	0.548	201.2 Da LogP 1.24 TPSA 76.0	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2cnccn2)cn1`
ZINC12360654 ZINC	0.545	207.2 Da LogP 1.30 TPSA 76.0	✓ Ro5	✓ Clean	`O=C(O)c1csc(-c2cnccn2)n1`
ZINC26423456 ZINC	0.543	250.2 Da LogP 0.88 TPSA 105.1	✓ Ro5	✓ Clean	`O=C(O)c1csc(NC(=O)c2cnccn2)n1`
ZINC220133900 ZINC	0.538	398.3 Da LogP 3.77 TPSA 85.1	✓ Ro5	✓ Clean	`Cc1nc2nc(-c3cccnc3)nn2cc1C(=O)Nc1cccc(C(F)(F)F)…`
ZINC20148987 ZINC	0.532	414.4 Da LogP 4.50 TPSA 97.1	✓ Ro5	✓ Clean	`Cc1ccc(C(=O)Nc2cccc(C(F)(F)F)c2)cc1Nc1cncc(C(N)…`
ZINC2580774 ZINC	0.531	216.3 Da LogP 2.41 TPSA 42.9	✓ Ro5	✓ Clean	`O=C(Sc1ccccc1)c1cnccn1`
ZINC4749098 ZINC	0.529	243.2 Da LogP 1.43 TPSA 92.2	✓ Ro5	✓ Clean	`O=C(O)c1ccc(NC(=O)c2cnccn2)cc1`
ZINC2747329 ZINC	0.516	300.3 Da LogP 0.21 TPSA 109.8	✓ Ro5	✓ Clean	`O=C(NCCCCNC(=O)c1cnccn1)c1cnccn1`
ZINC2747452 ZINC	0.516	286.3 Da LogP -0.18 TPSA 109.8	✓ Ro5	✓ Clean	`O=C(NCCCNC(=O)c1cnccn1)c1cnccn1`
ZINC19092783 ZINC	0.515	205.2 Da LogP 0.28 TPSA 63.2	✓ Ro5	✓ Clean	`O=C1CCN(C(=O)c2cnccn2)CC1`
ZINC40542019 ZINC	0.515	209.3 Da LogP 0.67 TPSA 46.1	✓ Ro5	✓ Clean	`O=C(c1cnccn1)N1CCSCC1`
ZINC54792854 ZINC	0.515	202.2 Da LogP 0.63 TPSA 88.9	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(-c2cnccn2)n1`
ZINC74212868 ZINC	0.515	201.2 Da LogP 1.24 TPSA 76.0	✓ Ro5	✓ Clean	`O=C(O)c1cccc(-c2cnccn2)n1`
ZINC79435988 ZINC	0.515	209.2 Da LogP -0.32 TPSA 83.4	✓ Ro5	✓ Clean	`CN(CC(=O)O)CC(=O)c1cnccn1`
ZINC96047318 ZINC	0.515	366.4 Da LogP 1.43 TPSA 92.2	✓ Ro5	✓ Clean	`O=C(c1cnccn1)N1CCC2(CC1)CCN(C(=O)c1cnccn1)CC2`
ZINC21953682 ZINC	0.514	235.2 Da LogP 0.41 TPSA 83.4	✓ Ro5	✓ Clean	`O=C(O)C1CCN(C(=O)c2cnccn2)CC1`
ZINC9306398 ZINC	0.512	398.3 Da LogP 3.77 TPSA 85.1	✓ Ro5	✓ Clean	`Cc1c(C(=O)Nc2cccc(C(F)(F)F)c2)cnc2nc(-c3cccnc3)…`
ZINC5049572 ZINC	0.507	336.3 Da LogP 4.22 TPSA 58.2	✓ Ro5	✓ Clean	`CC(=O)Nc1cc(C(=O)Nc2cccc(C(F)(F)F)c2)ccc1C`
ZINC72174470 ZINC	0.507	360.4 Da LogP 2.73 TPSA 93.4	✓ Ro5	✓ Clean	`Cn1ncc2c(NCCCNc3cccnc3)nc(-c3cccnc3)nc21`
ZINC72149792 ZINC	0.506	360.4 Da LogP 2.65 TPSA 93.4	✓ Ro5	✓ Clean	`Cc1cnccc1NCCNc1nc(-c2cccnc2)nc2c1cnn2C`
ZINC12982005 ZINC	0.500	221.2 Da LogP 0.17 TPSA 83.4	✓ Ro5	✓ Clean	`O=C(O)[C@@H]1CCCN1C(=O)c1cnccn1`
ZINC13208295 ZINC	0.500	200.2 Da LogP 1.12 TPSA 67.8	✓ Ro5	✓ Clean	`O=C(Nc1ccncc1)c1cnccn1`
ZINC20280834 ZINC	0.500	221.2 Da LogP 0.17 TPSA 83.4	✓ Ro5	✓ Clean	`O=C(O)[C@H]1CCCN1C(=O)c1cnccn1`
ZINC2755537 ZINC	0.500	328.4 Da LogP 0.99 TPSA 109.8	✓ Ro5	✓ Clean	`O=C(NCCCCCCNC(=O)c1cnccn1)c1cnccn1`
ZINC32004931 ZINC	0.500	202.2 Da LogP 1.85 TPSA 42.9	✓ Ro5	✓ Clean	`O=C(c1ccc(F)cc1)c1cnccn1`
ZINC35110503 ZINC	0.500	207.2 Da LogP 0.07 TPSA 66.3	✓ Ro5	✓ Clean	`O=C(c1cnccn1)N1CCC(O)CC1`
ZINC375500 ZINC	0.500	326.4 Da LogP 0.74 TPSA 109.8	✓ Ro5	✓ Clean	`O=C(NC1CCC(NC(=O)c2cnccn2)CC1)c1cnccn1`
ZINC37658100 ZINC	0.500	218.6 Da LogP 2.36 TPSA 42.9	✓ Ro5	✓ Clean	`O=C(c1ccc(Cl)cc1)c1cnccn1`
ZINC54856994 ZINC	0.500	202.2 Da LogP 0.63 TPSA 88.9	✓ Ro5	✓ Clean	`O=C(O)c1cnc(-c2cnccn2)nc1`
ZINC646774339 ZINC	0.500	231.3 Da LogP 1.74 TPSA 46.1	✓ Ro5	✓ Clean	`O=C(c1cnccn1)N1CCC(C2CC2)CC1`
ZINC77101491 ZINC	0.500	207.2 Da LogP -0.37 TPSA 83.4	✓ Ro5	✓ Clean	`O=C(O)C1CN(C(=O)c2cnccn2)C1`
ZINC96053972 ZINC	0.500	324.3 Da LogP 0.11 TPSA 92.2	✓ Ro5	✓ Clean	`O=C(c1cnccn1)N1CC2CN(C(=O)c3cnccn3)CC2C1`

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 A0A0H3GYF8

Chemistry

ChEMBL DXH ChEMBL DWT