Protein target profile

KP13_00468

Curved DNA-binding protein

Genome: KpKP13 Gene: AHE46798.1 cbpA 3D evidence: Experimental + ColabFold model UniProt A6TH30

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Length 305

Pocket druggability 0.437

Direct ligand evidence 0 8 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

Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. Moderate predicted binding pocket FPocket selected-pocket score 0.44. This supports review but is not experimental validation. Structure available Experimental + ColabFold model Ligand evidence via structure/bioactivity 0 structural and 2 bioactivity records.

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 (%): 54.688 Lower values reduce human off-target concern.
Human E-value: 8.75e-15
Gut microbiome similarity: 1.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 40.132 Higher values support similarity to known essential genes.
DEG E-value: 5.6599999999999994e-30 Smaller values mean stronger essential-gene similarity.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 84.92 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.437

Structure 3LZ8

Pocket Pocket 8

P2Rank

Structure 3LZ8

Pocket No pockets

ColabFold model

FPocket 0.705 · Pocket 18

P2Rank 0.252 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 61 / 4744 genomes with a hit

Prevalence 1.3%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MELKDYYAILGVQPTDDLKTIKTAYRRLARKYHPDVSKENDAEAKFKDLAEAWEVLKDEQRRAEYDQLWQHRNDPGFGRQRQTHEQSYSQQDFDDIFSSMFGQQAHQRRRQHAARGHDLEIEVAVFLEETLAEQTRTISYNLPVYNVFGMIESETPKTLNVKIPAGVVDGQRIRLKGQGTPGENGGPNGDLWLVIHIAPHPLFDIVGHNLEIVLPLAPWEAALGAKVTVPTLKESILLTVPPGSKAGQRLRIKGKGLVSKTHTGDLFAVIKIVMPPKPDEKARELWQQLAAAEASFDPRKTWGKA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

GO:0051082 Binding to an unfolded protein.
GO:0006457 The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

36 records

Show feature table

Start	End	DB	Term	Name
198	275	Gene3D	G3DSA:2.60.260.20	-
1	102	SUPERFAMILY	SSF46565	Chaperone J-domain
1	102	InterPro	IPR036869	Chaperone J-domain superfamily
118	277	CDD	cd10747	DnaJ_C
114	197	Gene3D	G3DSA:2.60.260.20	-
157	293	PANTHER	PTHR43096	DNAJ HOMOLOG 1, MITOCHONDRIAL-RELATED
4	61	SMART	SM00271	dnaj_3
4	61	InterPro	IPR001623	DnaJ domain
5	58	CDD	cd06257	DnaJ
5	58	InterPro	IPR001623	DnaJ domain
1	305	Hamap	MF_01154	Curved DNA-binding protein [cbpA].
1	305	InterPro	IPR023859	DNA-binding protein, curved-DNA
5	69	ProSiteProfiles	PS50076	dnaJ domain profile.
5	69	InterPro	IPR001623	DnaJ domain
203	286	SUPERFAMILY	SSF49493	HSP40/DnaJ peptide-binding domain
203	286	InterPro	IPR008971	HSP40/DnaJ peptide-binding
114	197	FunFam	G3DSA:2.60.260.20:FF:000008	Curved DNA-binding protein
5	66	Pfam	PF00226	DnaJ domain
5	66	InterPro	IPR001623	DnaJ domain
46	65	ProSitePatterns	PS00636	Nt-dnaJ domain signature.
46	65	InterPro	IPR018253	DnaJ domain, conserved site
25	40	PRINTS	PR00625	DnaJ domain signature
25	40	InterPro	IPR001623	DnaJ domain
7	25	PRINTS	PR00625	DnaJ domain signature
7	25	InterPro	IPR001623	DnaJ domain
41	61	PRINTS	PR00625	DnaJ domain signature
41	61	InterPro	IPR001623	DnaJ domain
61	80	PRINTS	PR00625	DnaJ domain signature
61	80	InterPro	IPR001623	DnaJ domain
114	207	SUPERFAMILY	SSF49493	HSP40/DnaJ peptide-binding domain
114	207	InterPro	IPR008971	HSP40/DnaJ peptide-binding
119	275	Pfam	PF01556	DnaJ C terminal domain
119	275	InterPro	IPR002939	Chaperone DnaJ, C-terminal
2	113	Gene3D	G3DSA:1.10.287.110	DnaJ domain
2	113	InterPro	IPR036869	Chaperone J-domain superfamily
276	305	Gene3D	G3DSA:1.20.5.460	Single helix bin

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 #8

0.437

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Surrounding area

Binding pockets · FPocket

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

Site 1 FPocket #18

0.705

Likely same site as P2Rank 3 3.3 Å 5 shared residues 83% of smaller site

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Surrounding area

Site 2 FPocket #1

0.349

Likely same site as P2Rank 1 5.3 Å 8 shared residues 67% 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

0.252

Likely same site as FPocket 1 5.3 Å 8 shared residues 67% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.052

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Surrounding area

Site 3 P2Rank #3

0.01

Likely same site as FPocket 18 3.3 Å 5 shared residues 83% of smaller site

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Surrounding area

All structural evidence 2 experimental · 1 predicted

Structural evidence

2 + 1

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
PDB 3I38	X-ray	—	A	—	PDBe RCSB PDBj File	Loaded
PDB 3LZ8	X-ray	—	A	—	PDBe RCSB PDBj File	Viewing
ColabFold KP13_00468	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.

8 records

Chemistry signal

Bioactivity evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 2 records from similar proteins

Structural ligands 0 0 loaded crystals

Measured bioactivity 2 direct and transferred ChEMBL records

Proposed compounds 6 similarity-based ZINC candidates

Best available ligand signal

DWT ChEMBL via homolog pchembl 9.09 (~0.8 nM) 503.5 Da · LogP 5.75 · TPSA 97.6 Open detail ChEMBL

CHEMBL4129274 ChEMBL via homolog Detail ChEMBL

ZINC71842002 ZINC proposed compound · Tanimoto 0.552 Detail ZINC

ZINC220133900 ZINC proposed compound · Tanimoto 0.538 Detail ZINC

ZINC20148987 ZINC proposed compound · Tanimoto 0.532 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.

No PDB ligands found through similar proteins.

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
DWT ChEMBL	Q9NXW2	9.09 ~0.8 nM	503.5 Da LogP 5.75 TPSA 97.6	2 viol.	✓ Clean	`Cc1ccc(cc1Nc2c3cn(nc3nc(n2)c4cccnc4)C)C(=O)Nc5c…`
CHEMBL4129274 ChEMBL	O75190	—	851.5 Da LogP 4.76 TPSA 183.3	3 viol.	Alert	`C=CC(=O)Nc1ccccc1Nc1nc(Nc2ccc(N3CCN(CCOCCOCCOCC…`

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
ZINC71842002 ZINC	0.552	445.6 Da LogP 2.04 TPSA 76.7	✓ Ro5	✓ Clean	`O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12)NCCCN1CC…`
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)…`
ZINC914431236 ZINC	0.531	464.0 Da LogP 4.49 TPSA 85.4	✓ Ro5	Alert	`C=CC(=O)Nc1ccccc1Nc1nc(Nc2ccc(N3CCN(C)CC3)cc2)n…`
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`

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.