Protein target profile

KP13_04589

Coenzyme PQQ synthesis protein B

Genome: KpKP13 Gene: pqqB AHE44464.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GT57

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Length 308

Pocket druggability 0.083

Direct ligand evidence 0 38 total records

Functional annotation 0 EC 1 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

Risks to review

Microbiome similarity 41 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 0.08.

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: No hit
Gut microbiome similarity: 0.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 0.0 Higher values support similarity to known essential genes.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 96.29 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 0.083

Structure A0A0H3GT57

Pocket Pocket 6

P2Rank 0.802

Structure A0A0H3GT57

Pocket Pocket 1

ColabFold model

FPocket 0.142 · Pocket 3

P2Rank 0.841 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 41 / 4744 genomes with a hit

Prevalence 0.9%

Cross-references

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

Sequence

UniProt A0A0H3GT57

Sequence

Primary amino-acid sequence viewer.

MFIKVLGSAAGGGFPQWNCNCANCQGLRDGTIQAAPRTQSSIIVSDNGKEWVLCNASPDISQQIAHTPELNKAGVLRGTHIGGIILTDSQIDHTTGLLSLREGCPHQVWCTPEVHEDLSTGFPVFTMLRHWNGGLVHHPIAPQQPFTVDACPDLQFTAVPIASNAPPYSPYRDRPLPGHNVALFIENRRNGQTLFYAPGLGEPDETLLPWLQKADCLLIDGTVWQDDELQAAGVGRNTGRDMGHLALGDEHGMMALLASLPAKRKILIHINNTNPILNEQSPQRQALTQQGIEVSWDGMAITLQDTAC

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

GO:0018189 The chemical reactions and pathways resulting in the formation of the cofactor pyrroloquinoline quinone (PQQ); it is synthesized from a small peptide containing tyrosine and glutamic acid; these amino acids in the peptide are multiply cross-linked and the rest of the peptide is removed.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

13 records

Show feature table

Start	End	DB	Term	Name
3	303	PANTHER	PTHR42663	HYDROLASE C777.06C-RELATED-RELATED
1	221	CDD	cd16274	PQQB-like_MBL-fold
1	221	InterPro	IPR011842	Coenzyme PQQ biosynthesis protein B
1	307	Gene3D	G3DSA:3.60.15.10	-
1	307	InterPro	IPR036866	Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
1	308	Hamap	MF_00653	Coenzyme PQQ synthesis protein B [pqqB].
1	308	InterPro	IPR011842	Coenzyme PQQ biosynthesis protein B
51	270	Pfam	PF12706	Beta-lactamase superfamily domain
51	270	InterPro	IPR001279	Metallo-beta-lactamase
1	303	SUPERFAMILY	SSF56281	Metallo-hydrolase/oxidoreductase
1	303	InterPro	IPR036866	Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
3	303	NCBIfam	TIGR02108	pyrroloquinoline quinone biosynthesis protein PqqB
3	303	InterPro	IPR011842	Coenzyme PQQ biosynthesis protein B

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

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

Site 1 P2Rank #1

0.802

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Surrounding area

Site 2 P2Rank #2

0.019

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Surrounding area

Site 3 P2Rank #3

0.004

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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

0.841

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Surrounding area

Site 2 P2Rank #2

0.025

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Surrounding area

Site 3 P2Rank #3

0.004

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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_A0A0H3GT57	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_04589	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.

38 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 2 records from similar proteins

Structural ligands 2 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 36 similarity-based ZINC candidates

Best available ligand signal

HKS PDB via homolog 316.3 Da · LogP -0.44 · TPSA 167.1 Open detail RCSB PDB

MLT PDB via homolog Detail RCSB PDB

ZINC71773889 ZINC proposed compound · Tanimoto 0.667 Detail ZINC

ZINC71773890 ZINC proposed compound · Tanimoto 0.667 Detail ZINC

ZINC71773891 ZINC proposed compound · Tanimoto 0.667 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
HKS RCSB PDB	6E13	Q88QV5	316.3 Da LogP -0.44 TPSA 167.1	1 viol.	Alert	`c1c(cc(c(c1O)O)SC[C@H](C(=O)O)N)C[C@@H](C(=O)O)N`
MLT RCSB PDB	4Z5Z	Q88QV5	134.1 Da LogP -1.09 TPSA 94.8	✓ Ro5	✓ Clean	`C([C@H](C(=O)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
ZINC71773889 ZINC	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@H](O)C(=O)O)C[C@H](O)C(=O)O`
ZINC71773890 ZINC	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@H](O)C(=O)O)C[C@@H](O)C(=O)O`
ZINC71773891 ZINC	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@@H](O)C(=O)O)C[C@@H](O)C(=O)O`
ZINC6091244 ZINC	0.595	217.2 Da LogP 0.62 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@@H](Cc1cc(F)c(O)c(F)c1)C(=O)O`
ZINC6091245 ZINC	0.595	217.2 Da LogP 0.62 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@H](Cc1cc(F)c(O)c(F)c1)C(=O)O`
ZINC79036542 ZINC	0.568	211.2 Da LogP -0.49 TPSA 135.6	✓ Ro5	✓ Clean	`Nc1cc(C[C@H](N)C(=O)O)cc(N)c1O`
ZINC1746050 ZINC	0.553	250.1 Da LogP 1.65 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@H](Cc1cc(Cl)c(O)c(Cl)c1)C(=O)O`
ZINC3861723 ZINC	0.553	433.0 Da LogP 1.56 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@@H](Cc1cc(I)c(O)c(I)c1)C(=O)O`
ZINC3875424 ZINC	0.553	433.0 Da LogP 1.56 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@H](Cc1cc(I)c(O)c(I)c1)C(=O)O`
ZINC57299 ZINC	0.553	339.0 Da LogP 1.87 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@@H](Cc1cc(Br)c(O)c(Br)c1)C(=O)O`
ZINC57300 ZINC	0.553	339.0 Da LogP 1.87 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@H](Cc1cc(Br)c(O)c(Br)c1)C(=O)O`
ZINC901726 ZINC	0.553	250.1 Da LogP 1.65 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@@H](Cc1cc(Cl)c(O)c(Cl)c1)C(=O)O`
ZINC2015200 ZINC	0.550	227.2 Da LogP 0.06 TPSA 113.0	✓ Ro5	✓ Clean	`COc1c(O)cc(C[C@H](N)C(=O)O)cc1O`
ZINC1577651 ZINC	0.526	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	0.526	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	0.526	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`
ZINC2382058 ZINC	0.526	219.2 Da LogP 1.06 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1cc(F)c(F)c(F)c1)C(=O)O`
ZINC2585943 ZINC	0.526	219.2 Da LogP 1.06 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1cc(F)c(F)c(F)c1)C(=O)O`
ZINC2570863 ZINC	0.523	270.3 Da LogP 0.85 TPSA 112.6	✓ Ro5	✓ Clean	`CC(=O)Nc1ccc(O)c(SC[C@H](N)C(=O)O)c1`
ZINC113771 ZINC	0.500	201.2 Da LogP 0.92 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1cc(F)cc(F)c1)C(=O)O`
ZINC113775 ZINC	0.500	201.2 Da LogP 0.92 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1cc(F)cc(F)c1)C(=O)O`
ZINC12428290 ZINC	0.500	271.2 Da LogP 0.16 TPSA 169.8	✓ Ro5	✓ Clean	`N[C@@H](Cc1cc([N+](=O)[O-])c(O)c([N+](=O)[O-])c…`
ZINC12428291 ZINC	0.500	271.2 Da LogP 0.16 TPSA 169.8	✓ Ro5	✓ Clean	`N[C@H](Cc1cc([N+](=O)[O-])c(O)c([N+](=O)[O-])c1…`
ZINC139322495 ZINC	0.500	225.2 Da LogP 0.66 TPSA 92.8	✓ Ro5	✓ Clean	`COc1c(C)cc(C[C@H](N)C(=O)O)cc1O`
ZINC1713868 ZINC	0.500	321.1 Da LogP 1.26 TPSA 83.6	✓ Ro5	✓ Clean	`Cc1cc(C[C@H](N)C(=O)O)cc(I)c1O`
ZINC17353379 ZINC	0.500	321.1 Da LogP 1.26 TPSA 83.6	✓ Ro5	✓ Clean	`Cc1cc(C[C@@H](N)C(=O)O)cc(I)c1O`
ZINC2512061 ZINC	0.500	360.4 Da LogP 0.67 TPSA 167.1	1 viol.	✓ Clean	`N[C@@H](Cc1ccc(O)c(-c2cc(C[C@H](N)C(=O)O)ccc2O)…`
ZINC32223593 ZINC	0.500	234.1 Da LogP 1.95 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1cc(Cl)cc(Cl)c1)C(=O)O`
ZINC44283977 ZINC	0.500	323.0 Da LogP 2.17 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1cc(Br)cc(Br)c1)C(=O)O`
ZINC44283979 ZINC	0.500	323.0 Da LogP 2.17 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1cc(Br)cc(Br)c1)C(=O)O`
ZINC59761244 ZINC	0.500	417.0 Da LogP 1.85 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1cc(I)cc(I)c1)C(=O)O`
ZINC6091327 ZINC	0.500	234.1 Da LogP 1.95 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1cc(Cl)cc(Cl)c1)C(=O)O`
ZINC6091882 ZINC	0.500	360.4 Da LogP 0.67 TPSA 167.1	1 viol.	✓ Clean	`N[C@@H](Cc1ccc(O)c(-c2cc(C[C@@H](N)C(=O)O)ccc2O…`
ZINC6091894 ZINC	0.500	360.4 Da LogP 0.67 TPSA 167.1	1 viol.	✓ Clean	`N[C@H](Cc1ccc(O)c(-c2cc(C[C@@H](N)C(=O)O)ccc2O)…`
ZINC96029416 ZINC	0.500	235.6 Da LogP 1.57 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1cc(F)c(Cl)c(F)c1)C(=O)O`
ZINC96029417 ZINC	0.500	235.6 Da LogP 1.57 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1cc(F)c(Cl)c(F)c1)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.