Protein profile

PA5000

alpha-1,3-rhamnosyltransferase WapR

Genome: NC_002516.2

Gene: wapR PA5000 Structure source: AlphaFold UniProt Q9HUG5

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Amino acids 294

Annotations 7

Features 7

PDB binders 3

Druggability 0.86

Overview

Basic information about this protein and its source genome.

Accession: PA5000
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: wapR PA5000
Status: annotated
Amino acids: 294
Structure source: AlphaFold

GO:0016757 Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor). GO:0016758 Catalysis of the transfer of a hexosyl group from one compound (donor) to another (acceptor). GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. GO:0009244 The chemical reactions and pathways resulting in the formation of the core region of bacterial lipopolysaccharides, which contains ten saccharide residues. GO:0015920 The directed movement of lipopolysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A lipopolysaccharide is any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria. Lipopolysaccharides consist three covalently linked regions, lipid A, core oligosaccharide, and an O side chain. Lipid A is responsible for the toxicity of the lipopolysaccharide. GO:0009243 The chemical reactions and pathways resulting in the formation of the O side chain of a lipopolysaccharide, which determines the antigenic specificity of the organism. It is made up of about 50 repeating units of a branched tetrasaccharide.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 22.481
Human E-value: 6.32e-07
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: CytoplasmicMembrane

Selected Druggability evidence

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 0.86

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

GO:0016757 Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
GO:0016758 Catalysis of the transfer of a hexosyl group from one compound (donor) to another (acceptor).
GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
GO:0009244 The chemical reactions and pathways resulting in the formation of the core region of bacterial lipopolysaccharides, which contains ten saccharide residues.
GO:0015920 The directed movement of lipopolysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A lipopolysaccharide is any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria. Lipopolysaccharides consist three covalently linked regions, lipid A, core oligosaccharide, and an O side chain. Lipid A is responsible for the toxicity of the lipopolysaccharide.
GO:0009243 The chemical reactions and pathways resulting in the formation of the O side chain of a lipopolysaccharide, which determines the antigenic specificity of the organism. It is made up of about 50 repeating units of a branched tetrasaccharide.
GO:0044010 A process in which planktonically growing microorganisms of the same species grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.

Sequence Features

Domain/signature hits from InterPro and related databases.

7 records

Show feature table

Start	End	DB	Term	Name
13	180	Pfam	PF00535	Glycosyl transferase family 2
13	180	InterPro	IPR001173	Glycosyltransferase 2-like
8	225	SUPERFAMILY	SSF53448	Nucleotide-diphospho-sugar transferases
8	225	InterPro	IPR029044	Nucleotide-diphospho-sugar transferases
3	256	Gene3D	G3DSA:3.90.550.10	Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
3	256	InterPro	IPR029044	Nucleotide-diphospho-sugar transferases
8	222	PANTHER	PTHR22916	GLYCOSYLTRANSFERASE

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

0 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA5000	AlphaFold	—	—	full sequence	—	Viewing

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
1				0.585
2				0.406

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.

56 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
TYD	1H7Q	P39621	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…`
UD2	2Z87	Q8L0V4	607.4 Da LogP -4.65 TPSA 305.9	3 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@H]([C@H]([C@H](O[C@@H]1O[P@@](…`
UGA	2Z86	Q8L0V4	580.3 Da LogP -4.70 TPSA 314.1	3 viol.	✓ Clean	`C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…`

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
CHEMBL1817949	Q8KHG4	—	591.4 Da LogP -3.62 TPSA 285.6	3 viol.	✓ Clean	`CC(=O)N[C@H]1[C@@H](OP(=O)(O)OP(=O)(O)OC[C@H]2O…`
CHEMBL447878	B1B4J9	—	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@H]…`
NGA	B1B4J9	—	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@H]([C@H]([C@H](O[C@H]1O)CO)O)O`

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
ZINC895331	1.000	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)[C@@H](O)[C@H](CO)O[C@H]1O`
ZINC17107637	0.769	320.2 Da LogP -1.46 TPSA 162.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@@H](COP(N)(N)=O)O2)c(…`
ZINC17107641	0.769	320.2 Da LogP -1.46 TPSA 162.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](COP(N)(N)=O)O2)c(=…`
ZINC5493427	0.769	320.2 Da LogP -1.46 TPSA 162.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](COP(N)(N)=O)O2)c(=O…`
ZINC5493430	0.769	320.2 Da LogP -1.46 TPSA 162.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](COP(N)(N)=O)O2)c(=…`
ZINC205444277	0.735	223.2 Da LogP -2.10 TPSA 99.0	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)O[C@H](CO)[C@@H](F)[C@@H]…`
ZINC255996057	0.735	223.2 Da LogP -2.10 TPSA 99.0	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@H](O)[C@@H](F)[C@@H](CO)O[C@H]1O`
ZINC255996058	0.735	223.2 Da LogP -2.10 TPSA 99.0	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)O[C@H](CO)[C@H](F)[C@@H]1O`
ZINC255996059	0.735	223.2 Da LogP -2.10 TPSA 99.0	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@H](O)[C@H](F)[C@@H](CO)O[C@H]1O`
ZINC38917814	0.735	223.2 Da LogP -2.10 TPSA 99.0	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[C@@H](F)[C@@H]…`
ZINC38917815	0.735	223.2 Da LogP -2.10 TPSA 99.0	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](F)[C@@H]1O`
ZINC1569985092	0.730	381.4 Da LogP -4.59 TPSA 189.2	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)O[C@H](CO)[C@H](C[C@@H]2O…`
ZINC1569985093	0.730	381.4 Da LogP -4.59 TPSA 189.2	1 viol.	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)[C@@H](C[C@@H]2O[C@H](CO)…`
ZINC1569985094	0.730	381.4 Da LogP -4.59 TPSA 189.2	1 viol.	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)[C@@H](C[C@@H]2O[C@H](CO)…`
ZINC1569985095	0.730	381.4 Da LogP -4.59 TPSA 189.2	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)O[C@H](CO)[C@H](C[C@@H]2O…`
ZINC2362797652	0.714	246.2 Da LogP -1.76 TPSA 147.8	✓ Ro5	Alert	`CC(=O)N[C@H]1[C@H](O)O[C@H](CN=[N+]=[N-])[C@@H]…`
ZINC66097452	0.714	246.2 Da LogP -1.76 TPSA 147.8	✓ Ro5	Alert	`CC(=O)N[C@H]1[C@@H](O)O[C@H](CN=[N+]=[N-])[C@@H…`
ZINC16969385	0.706	235.2 Da LogP -2.69 TPSA 119.3	✓ Ro5	✓ Clean	`CCC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]…`
ZINC1857790104	0.706	235.2 Da LogP -2.69 TPSA 119.3	✓ Ro5	✓ Clean	`CCC(=O)N[C@H]1[C@H](O)[C@@H](O)[C@H](CO)O[C@H]1O`
ZINC225208891	0.706	236.2 Da LogP -3.28 TPSA 131.3	1 viol.	✓ Clean	`CNC(=O)N[C@@H]1[C@H](O)O[C@H](CO)[C@H](O)[C@@H]…`
ZINC2527936	0.706	235.2 Da LogP -2.69 TPSA 119.3	✓ Ro5	✓ Clean	`CCC(=O)N[C@@H]1[C@@H](O)O[C@@H](CO)[C@H](O)[C@H…`
ZINC253389827	0.706	236.2 Da LogP -3.28 TPSA 131.3	1 viol.	✓ Clean	`CNC(=O)N[C@H]1[C@H](O)[C@H](O)[C@@H](CO)O[C@H]1O`
ZINC253389828	0.706	236.2 Da LogP -3.28 TPSA 131.3	1 viol.	✓ Clean	`CNC(=O)N[C@@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H…`
ZINC253389829	0.706	236.2 Da LogP -3.28 TPSA 131.3	1 viol.	✓ Clean	`CNC(=O)N[C@H]1[C@H](O)[C@@H](O)[C@@H](CO)O[C@H]…`
ZINC25721491	0.706	236.2 Da LogP -3.28 TPSA 131.3	1 viol.	✓ Clean	`CNC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[C@@H](O)[C@@H…`
ZINC25721497	0.706	236.2 Da LogP -3.28 TPSA 131.3	1 viol.	✓ Clean	`CNC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]…`
ZINC25721524	0.706	237.2 Da LogP -2.86 TPSA 128.5	✓ Ro5	✓ Clean	`COC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]…`
ZINC34218230	0.706	235.2 Da LogP -2.69 TPSA 119.3	✓ Ro5	✓ Clean	`CCC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[C@@H](O)[C@@H…`
ZINC38392638	0.706	235.2 Da LogP -2.69 TPSA 119.3	✓ Ro5	✓ Clean	`CCC(=O)N[C@@H]1[C@@H](O)O[C@H](CO)[C@@H](O)[C@@…`
ZINC38392639	0.706	235.2 Da LogP -2.69 TPSA 119.3	✓ Ro5	✓ Clean	`CCC(=O)N[C@@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H…`
ZINC4692106	0.706	235.2 Da LogP -2.69 TPSA 119.3	✓ Ro5	✓ Clean	`CCC(=O)N[C@H]1[C@@H](O)O[C@@H](CO)[C@@H](O)[C@H…`
ZINC4692107	0.706	235.2 Da LogP -2.69 TPSA 119.3	✓ Ro5	✓ Clean	`CCC(=O)N[C@@H]1[C@@H](O)O[C@@H](CO)[C@@H](O)[C@…`
ZINC4692108	0.706	235.2 Da LogP -2.69 TPSA 119.3	✓ Ro5	✓ Clean	`CCC(=O)N[C@H]1[C@@H](O)O[C@@H](CO)[C@@H](O)[C@@…`
ZINC4692109	0.706	235.2 Da LogP -2.69 TPSA 119.3	✓ Ro5	✓ Clean	`CCC(=O)N[C@@H]1[C@@H](O)O[C@@H](CO)[C@@H](O)[C@…`
ZINC6667024	0.706	256.3 Da LogP -0.86 TPSA 93.5	✓ Ro5	✓ Clean	`COC[C@H]1O[C@@H](n2cc(C)c(=O)[nH]c2=O)C[C@@H]1O`
ZINC6792406	0.706	236.2 Da LogP -3.28 TPSA 131.3	1 viol.	✓ Clean	`CNC(=O)N[C@H]1[C@@H](O)O[C@@H](CO)[C@@H](O)[C@H…`
ZINC6792408	0.706	236.2 Da LogP -3.28 TPSA 131.3	1 viol.	✓ Clean	`CNC(=O)N[C@H]1[C@@H](O)O[C@@H](CO)[C@@H](O)[C@@…`
ZINC6792411	0.706	236.2 Da LogP -3.28 TPSA 131.3	1 viol.	✓ Clean	`CNC(=O)N[C@@H]1[C@@H](O)O[C@@H](CO)[C@@H](O)[C@…`
ZINC6792412	0.706	236.2 Da LogP -3.28 TPSA 131.3	1 viol.	✓ Clean	`CNC(=O)N[C@@H]1[C@@H](O)O[C@@H](CO)[C@@H](O)[C@…`
ZINC1532902	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC409415373	0.697	222.2 Da LogP -3.55 TPSA 145.3	1 viol.	✓ Clean	`NC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[C@H](O)[C@@H]1O`
ZINC409415374	0.697	222.2 Da LogP -3.55 TPSA 145.3	1 viol.	✓ Clean	`NC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@H](O)[C@@H]1O`
ZINC12959005	0.694	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@](=O)(O)…`
ZINC12959016	0.694	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@](=O)(O)O[P@](=O)(O…`
ZINC25726233	0.694	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@](=O)(O)O[P@](=O)(O)…`
ZINC3861755	0.694	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC3875255	0.694	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC3875256	0.694	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)…`
ZINC88466482	0.694	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=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.