Protein profile

KP13_04589

Coenzyme PQQ synthesis protein B

Genome: KpKP13

Gene: AHE44464.1 pqqB Structure source: AlphaFold + ColabFold UniProt A0A0H3GT57

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Amino acids 308

Annotations 1

Features 13

PDB binders 2

Druggability 0.083

Overview

Basic information about this protein and its source genome.

Accession: KP13_04589
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44464.1 pqqB
Status: annotated
Amino acids: 308
Structure source: AlphaFold + ColabFold

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.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 96.29

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its 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

Normalized 0.009

Sequence

Primary amino-acid sequence viewer.

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GT57	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04589	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				12.03	0.636
2				1.04	0.006

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				13.34	0.683

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

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, 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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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.