Protein profile

KP13_00473

Biofilm PGA synthesis lipoprotein pgaB

Genome: KpKP13

Gene: pgaB AHE46793.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GL72

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Amino acids 673

Annotations 3

Features 19

PDB binders 1

Druggability 0.508

Overview

Basic information about this protein and its source genome.

Accession: KP13_00473
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: pgaB AHE46793.1
Status: annotated
Amino acids: 673
Structure source: AlphaFold + ColabFold

GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. GO:0043708 The attachment of a cell to a solid substrate, via cell adhesion molecules, contributing to the formation of a biofilm. GO:0016810 Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 52.906
DEG E-value: 0.0
Localization: Periplasmic
ColabFold pLDDT: 93.84

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 0.508

Structure A0A0H3GL72

Pocket Pocket 39

P2Rank 0.911

Structure A0A0H3GL72

Pocket Pocket 1

ColabFold model

FPocket 0.83 · Pocket 46

P2Rank 0.909 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 51 / 4744 genomes with a hit

Normalized 0.011

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
GO:0043708 The attachment of a cell to a solid substrate, via cell adhesion molecules, contributing to the formation of a biofilm.
GO:0016810 Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.

Sequence Features

Domain/signature hits from InterPro and related databases.

19 records

Show feature table

Start	End	DB	Term	Name
26	324	PANTHER	PTHR34216	-
27	673	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
105	272	Pfam	PF01522	Polysaccharide deacetylase
105	272	InterPro	IPR002509	NodB homology domain
23	26	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	26	SignalP_EUK	SignalP-noTM	SignalP-noTM
1	10	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
311	673	Gene3D	G3DSA:3.20.20.80	Glycosidases
50	666	NCBIfam	TIGR03938	poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB
50	666	InterPro	IPR023854	Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB
1	26	Phobius	SIGNAL_PEPTIDE	Signal peptide region
11	22	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
320	646	Pfam	PF14883	Hypothetical glycosyl hydrolase family 13
320	646	InterPro	IPR032772	Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, C-terminal
109	351	ProSiteProfiles	PS51677	NodB homology domain profile.
109	351	InterPro	IPR002509	NodB homology domain
68	307	SUPERFAMILY	SSF88713	Glycoside hydrolase/deacetylase
68	307	InterPro	IPR011330	Glycoside hydrolase/deacetylase, beta/alpha-barrel
44	310	Gene3D	G3DSA:3.20.20.370	Glycoside hydrolase/deacetylase

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_A0A0H3GL72	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00473	ColabFold	—	—	full sequence	—	Loaded

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

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
2				0.011
1				0.002
9				0.001
35				0.0

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	Score	Probability
1	31.61	0.911
2	12.0	0.549
3	9.66	0.447
4	5.54	0.219
5	3.25	0.09

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
46				0.83

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	Score	Probability
1	22.11	0.877
2	7.95	0.423
3	6.79	0.347
4	5.6	0.269
5	2.4	0.064

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.

51 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
GCS	4P7N	P75906	179.2 Da LogP -3.25 TPSA 116.2	✓ Ro5	✓ Clean	`C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)N)O)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
ZINC2060993438	0.656	340.3 Da LogP -5.46 TPSA 201.1	2 viol.	✓ Clean	`N[C@@H]1[C@@H](O)O[C@@H](CO)[C@H](O[C@H]2O[C@@H…`
ZINC2060993439	0.656	340.3 Da LogP -5.46 TPSA 201.1	2 viol.	✓ Clean	`N[C@@H]1[C@H](O)O[C@H](CO)[C@H](O[C@H]2O[C@H](C…`
ZINC2060993440	0.656	340.3 Da LogP -5.46 TPSA 201.1	2 viol.	✓ Clean	`N[C@H]1[C@H](O)[C@@H](O[C@H]2O[C@H](CO)[C@H](O)…`
ZINC2060993441	0.656	340.3 Da LogP -5.46 TPSA 201.1	2 viol.	✓ Clean	`N[C@@H]1[C@@H](O[C@H]2[C@@H](CO)O[C@@H](O)[C@@H…`
ZINC2060993442	0.656	340.3 Da LogP -5.46 TPSA 201.1	2 viol.	✓ Clean	`N[C@H]1[C@H](O)[C@@H](O[C@H]2O[C@H](CO)[C@H](O)…`
ZINC255997143	0.656	340.3 Da LogP -5.46 TPSA 201.1	2 viol.	✓ Clean	`N[C@@H]1[C@H](O[C@@H]2[C@H](CO)O[C@H](O)[C@H](N…`
ZINC255997144	0.656	340.3 Da LogP -5.46 TPSA 201.1	2 viol.	✓ Clean	`N[C@@H]1[C@H](O[C@@H]2[C@H](CO)O[C@H](O)[C@H](N…`
ZINC25723126	0.656	340.3 Da LogP -5.46 TPSA 201.1	2 viol.	✓ Clean	`N[C@H]1[C@H](O[C@@H]2[C@@H](CO)O[C@@H](O)[C@H](…`
ZINC4535916	0.656	340.3 Da LogP -5.46 TPSA 201.1	2 viol.	✓ Clean	`N[C@@H]1[C@H](O[C@@H]2[C@H](CO)O[C@H](O)[C@H](N…`
ZINC4535920	0.656	340.3 Da LogP -5.46 TPSA 201.1	2 viol.	✓ Clean	`N[C@@H]1[C@H](O[C@@H]2[C@H](CO)O[C@H](O)[C@H](N…`
ZINC64219075	0.656	340.3 Da LogP -5.46 TPSA 201.1	2 viol.	✓ Clean	`N[C@H]1[C@H](O[C@@H]2[C@@H](CO)O[C@@H](O)[C@H](…`
ZINC64219076	0.656	340.3 Da LogP -5.46 TPSA 201.1	2 viol.	✓ Clean	`N[C@H]1[C@H](O[C@@H]2[C@H](CO)O[C@@H](O)[C@H](N…`
ZINC64219079	0.656	340.3 Da LogP -5.46 TPSA 201.1	2 viol.	✓ Clean	`N[C@H]1[C@H](O[C@@H]2[C@H](CO)O[C@@H](O)[C@H](N…`
ZINC64624873	0.656	340.3 Da LogP -5.46 TPSA 201.1	2 viol.	✓ Clean	`N[C@H]1[C@H](O[C@@H]2[C@@H](CO)O[C@H](O)[C@H](N…`
ZINC34007792	0.606	341.3 Da LogP -5.43 TPSA 195.3	2 viol.	✓ Clean	`N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O[C@@H]2O[C@H](…`
ZINC34577641	0.606	341.3 Da LogP -5.43 TPSA 195.3	2 viol.	✓ Clean	`N[C@H]1[C@@H](O)O[C@H](CO)[C@@H](O[C@@H]2O[C@H]…`
ZINC34328190	0.529	259.2 Da LogP -3.43 TPSA 159.5	✓ Ro5	✓ Clean	`N[C@H]1[C@@H](O)O[C@H](CO)[C@@H](O)[C@@H]1OS(=O…`
ZINC43763932	0.529	259.2 Da LogP -3.43 TPSA 159.5	✓ Ro5	✓ Clean	`N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]1OS(=O)…`
ZINC13543969	0.515	259.2 Da LogP -3.43 TPSA 159.5	✓ Ro5	✓ Clean	`N[C@H]1[C@@H](O)O[C@H](COS(=O)(=O)O)[C@@H](O)[C…`
ZINC257487053	0.515	259.2 Da LogP -3.43 TPSA 159.5	✓ Ro5	✓ Clean	`N[C@H]1[C@H](O)[C@H](O)[C@@H](COS(=O)(=O)O)O[C@…`
ZINC257487054	0.515	259.2 Da LogP -3.43 TPSA 159.5	✓ Ro5	✓ Clean	`N[C@H]1[C@H](O)[C@@H](O)[C@@H](COS(=O)(=O)O)O[C…`
ZINC4097102	0.515	259.2 Da LogP -3.14 TPSA 162.7	1 viol.	✓ Clean	`N[C@H]1[C@H](O)O[C@H](COP(=O)(O)O)[C@@H](O)[C@@…`
ZINC4097103	0.515	259.2 Da LogP -3.14 TPSA 162.7	1 viol.	✓ Clean	`N[C@H]1[C@@H](O)O[C@H](COP(=O)(O)O)[C@@H](O)[C@…`
ZINC5178949	0.515	259.2 Da LogP -3.43 TPSA 159.5	✓ Ro5	✓ Clean	`N[C@H]1[C@H](O)O[C@H](COS(=O)(=O)O)[C@@H](O)[C@…`
ZINC5829843	0.515	259.2 Da LogP -3.43 TPSA 159.5	✓ Ro5	✓ Clean	`N[C@@H]1[C@H](O)O[C@H](COS(=O)(=O)O)[C@H](O)[C@…`
ZINC5829963	0.515	259.2 Da LogP -3.43 TPSA 159.5	✓ Ro5	✓ Clean	`N[C@@H]1[C@H](O)O[C@H](COS(=O)(=O)O)[C@@H](O)[C…`
ZINC2061000428	0.514	251.2 Da LogP -2.76 TPSA 142.5	✓ Ro5	✓ Clean	`C[C@H](O[C@H]1[C@H](N)[C@H](O)O[C@@H](CO)[C@@H]…`
ZINC2061000429	0.514	251.2 Da LogP -2.76 TPSA 142.5	✓ Ro5	✓ Clean	`C[C@H](O[C@H]1[C@H](N)[C@@H](O)O[C@@H](CO)[C@@H…`
ZINC254624555	0.514	251.2 Da LogP -2.76 TPSA 142.5	✓ Ro5	✓ Clean	`C[C@H](O[C@@H]1[C@H](N)[C@H](O)O[C@@H](CO)[C@@H…`
ZINC254624558	0.514	251.2 Da LogP -2.76 TPSA 142.5	✓ Ro5	✓ Clean	`C[C@H](O[C@H]1[C@H](O)[C@H](CO)O[C@@H](O)[C@H]1…`
ZINC254624561	0.514	251.2 Da LogP -2.76 TPSA 142.5	✓ Ro5	✓ Clean	`C[C@H](O[C@@H]1[C@H](N)[C@H](O)O[C@H](CO)[C@H]1…`
ZINC3861271	0.514	251.2 Da LogP -2.76 TPSA 142.5	✓ Ro5	✓ Clean	`C[C@@H](O[C@H]1[C@H](O)[C@@H](CO)O[C@H](O)[C@@H…`
ZINC4097160	0.514	251.2 Da LogP -2.76 TPSA 142.5	✓ Ro5	✓ Clean	`C[C@@H](O[C@H]1[C@H](O)[C@@H](CO)O[C@@H](O)[C@@…`
ZINC4521704	0.514	251.2 Da LogP -2.76 TPSA 142.5	✓ Ro5	✓ Clean	`C[C@H](O[C@H]1[C@H](O)[C@@H](CO)O[C@H](O)[C@@H]…`
ZINC5706548	0.514	251.2 Da LogP -2.76 TPSA 142.5	✓ Ro5	✓ Clean	`C[C@H](O[C@@H]1[C@H](N)[C@H](O)O[C@H](CO)[C@@H]…`
ZINC5706549	0.514	251.2 Da LogP -2.76 TPSA 142.5	✓ Ro5	✓ Clean	`C[C@@H](O[C@@H]1[C@H](N)[C@H](O)O[C@H](CO)[C@@H…`
ZINC5706550	0.514	251.2 Da LogP -2.76 TPSA 142.5	✓ Ro5	✓ Clean	`C[C@H](O[C@H]1[C@H](N)[C@H](O)O[C@H](CO)[C@@H]1…`
ZINC5706551	0.514	251.2 Da LogP -2.76 TPSA 142.5	✓ Ro5	✓ Clean	`C[C@@H](O[C@H]1[C@H](N)[C@H](O)O[C@H](CO)[C@@H]…`
ZINC104897294	0.500	259.2 Da LogP -3.14 TPSA 162.7	1 viol.	✓ Clean	`N[C@@H]1[C@H](OP(=O)(O)O)O[C@H](CO)[C@@H](O)[C@…`
ZINC12503055	0.500	259.2 Da LogP -3.14 TPSA 162.7	1 viol.	✓ Clean	`N[C@H]1[C@@H](OP(=O)(O)O)O[C@H](CO)[C@H](O)[C@@…`
ZINC203488208	0.500	207.2 Da LogP -2.65 TPSA 93.4	✓ Ro5	✓ Clean	`CN(C)[C@@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC256013684	0.500	259.2 Da LogP -3.14 TPSA 162.7	1 viol.	✓ Clean	`N[C@@H]1[C@H](OP(=O)(O)O)O[C@H](CO)[C@H](O)[C@H…`
ZINC257346191	0.500	207.2 Da LogP -2.65 TPSA 93.4	✓ Ro5	✓ Clean	`CN(C)[C@H]1[C@H](O)[C@@H](O)[C@@H](CO)O[C@H]1O`
ZINC257346192	0.500	207.2 Da LogP -2.65 TPSA 93.4	✓ Ro5	✓ Clean	`CN(C)[C@H]1[C@H](O)[C@H](O)[C@@H](CO)O[C@H]1O`
ZINC257357488	0.500	341.3 Da LogP -5.43 TPSA 195.3	2 viol.	✓ Clean	`N[C@H]1[C@@H](O)[C@H](CO)O[C@@H](O[C@H]2O[C@@H]…`
ZINC257357489	0.500	341.3 Da LogP -5.43 TPSA 195.3	2 viol.	✓ Clean	`N[C@@H]1[C@H](O)[C@H](CO)O[C@@H](O[C@H]2O[C@@H]…`
ZINC257357490	0.500	341.3 Da LogP -5.43 TPSA 195.3	2 viol.	✓ Clean	`N[C@@H]1[C@@H](O)[C@H](CO)O[C@@H](O[C@H]2O[C@@H…`
ZINC3869944	0.500	259.2 Da LogP -3.14 TPSA 162.7	1 viol.	✓ Clean	`N[C@@H]1[C@H](OP(=O)(O)O)O[C@H](CO)[C@H](O)[C@@…`
ZINC3869946	0.500	259.2 Da LogP -3.14 TPSA 162.7	1 viol.	✓ Clean	`N[C@@H]1[C@H](OP(=O)(O)O)O[C@H](CO)[C@@H](O)[C@…`
ZINC4097029	0.500	259.2 Da LogP -3.14 TPSA 162.7	1 viol.	✓ Clean	`N[C@H]1[C@@H](OP(=O)(O)O)O[C@H](CO)[C@@H](O)[C@…`

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.