Protein profile

PA4209

phenazine-specific methyltransferase

Genome: NC_002516.2

Gene: PA4209 phzM Structure source: Experimental + AlphaFold UniProt Q9HWH2

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Amino acids 334

Annotations 10

Features 18

PDB binders 11

Druggability 0.73

Overview

Basic information about this protein and its source genome.

Accession: PA4209
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA4209 phzM
Status: annotated
Amino acids: 334
Structure source: Experimental + AlphaFold

2.1.1.327

GO:0102168 Catalysis of the reaction: phenazine-1-carboxylate + S-adenosyl-L-methionine = 5-methyl-phenazine-1-carboxylate + S-adenosyl-L-homocysteine. GO:0042802 Binding to an identical protein or proteins. GO:0008171 Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule. GO:0042803 Binding to an identical protein to form a homodimer. GO:1904047 Binding to S-adenosyl-L-methionine. GO:0008757 Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 22.552
Human E-value: 2.04e-10
Gut microbiome off-target: hit
Essential (DEG): N
Localization: Cytoplasmic

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 0.73

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

2.1.1.327

Gene Ontology (GO)

GO:0102168 Catalysis of the reaction: phenazine-1-carboxylate + S-adenosyl-L-methionine = 5-methyl-phenazine-1-carboxylate + S-adenosyl-L-homocysteine.
GO:0042802 Binding to an identical protein or proteins.
GO:0008171 Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.
GO:0042803 Binding to an identical protein to form a homodimer.
GO:1904047 Binding to S-adenosyl-L-methionine.
GO:0008757 Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
GO:0032259 The process in which a methyl group is covalently attached to a molecule.
GO:0106220 The chemical reactions and pathways resulting in the formation of pyrocyanin, an iminium betaine that is 5-methylphenazin-5-ium which is substituted at position 1 by an oxidanidyl group.
GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
10	89	SUPERFAMILY	SSF46785	Winged helix DNA-binding domain
10	89	InterPro	IPR036390	Winged helix DNA-binding domain superfamily
12	330	PANTHER	PTHR43712	PUTATIVE (AFU_ORTHOLOGUE AFUA_4G14580)-RELATED
12	330	InterPro	IPR016461	O-methyltransferase COMT-type
1	332	PIRSF	PIRSF005739	O-mtase
1	332	InterPro	IPR016461	O-methyltransferase COMT-type
1	88	Gene3D	G3DSA:1.10.10.10	-
1	88	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily
12	86	Pfam	PF16864	Dimerisation domain
12	86	InterPro	IPR031725	Acetylserotonin O-methyltransferase, dimerisation domain
95	330	SUPERFAMILY	SSF53335	S-adenosyl-L-methionine-dependent methyltransferases
95	330	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
89	334	Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39
89	334	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
13	333	ProSiteProfiles	PS51683	SAM-dependent O-methyltransferase class II-type profile.
13	333	InterPro	IPR016461	O-methyltransferase COMT-type
115	314	Pfam	PF00891	O-methyltransferase domain
115	314	InterPro	IPR001077	O-methyltransferase domain

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

1 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 2IP2	X-ray	1.80 Å	A,B	100.0% 1-334	PDBe RCSB PDBj File	Viewing
AlphaFold PA4209	AlphaFold	—	—	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				0.73

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	25.39	0.906
2	7.14	0.371
3	3.83	0.149
4	3.35	0.119

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				0.809

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.

61 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
3VL	4WXH	Q06528	569.6 Da LogP 2.16 TPSA 163.1	2 viol.	Alert	`CC[C@]1(C[C@@H](c2c(cc3c(c2O)C(=O)c4c(cccc4O)C3…`
4MU	5JR3	Q06528	176.2 Da LogP 1.81 TPSA 50.4	✓ Ro5	✓ Clean	`CC1=CC(=O)Oc2c1ccc(c2)O`
8B6	5XOH	A0A166U5H3	202.2 Da LogP 2.24 TPSA 63.6	✓ Ro5	✓ Clean	`c1coc2c1c(c3c(c2)OC(=O)C=C3)O`
DRA	1XDS	Q54527	769.8 Da LogP 2.93 TPSA 211.0	2 viol.	Alert	`CC[C@]1(C[C@@H](c2c(cc3c(c2O)C(=O)c4c(cccc4O)C3…`
ERT	1TW2	Q06528	599.6 Da LogP 2.17 TPSA 172.3	2 viol.	Alert	`CC[C@]1(C[C@@H](c2c(c(c3c(c2O)C(=O)c4c(cccc4OC)…`
HMO	1FP2	O24529	268.3 Da LogP 3.17 TPSA 59.7	✓ Ro5	✓ Clean	`COc1ccc2c(c1)OC=C(C2=O)c3ccc(cc3)O`
MQA	3GXO	Q9X5T6	349.3 Da LogP -0.96 TPSA 130.1	✓ Ro5	Alert	`CC1=C(C(=O)C2=C(C1=O)[N@@]3C[C@H]4[C@@H]([C@@]3…`
P9P	5EEH	Q06528	173.6 Da LogP 1.95 TPSA 63.4	✓ Ro5	✓ Clean	`c1cc(c(cc1N(=O)=O)Cl)O`
S8M	5EEG	Q06528	408.4 Da LogP -1.64 TPSA 199.8	1 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
SFG	1XDU	Q54527	381.4 Da LogP -2.06 TPSA 208.7	2 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
T3A	6CIG	O24529	243.3 Da LogP -2.43 TPSA 127.1	✓ Ro5	✓ Clean	`C(CNC(CO)(CO)CO)CS(=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
ZINC13650200	1.000	381.4 Da LogP -2.06 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@H](N)CC[C@H](N)…`
ZINC1611594	1.000	243.3 Da LogP -2.43 TPSA 127.1	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC(CO)(CO)CO`
ZINC205994753	1.000	381.4 Da LogP -2.06 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@H](N)CC[C@H](N)…`
ZINC205994774	1.000	381.4 Da LogP -2.06 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@H](N)CC[C@H](N)…`
ZINC27723577	1.000	381.4 Da LogP -2.06 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@H](N)CC[C@H](N)…`
ZINC38144766	1.000	349.3 Da LogP -0.96 TPSA 130.1	✓ Ro5	Alert	`COC1=C(C)C(=O)C2=C(C1=O)[C@@H](COC(N)=O)[C@@]1(…`
ZINC38192471	1.000	381.4 Da LogP -2.06 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@H](N)CC[C@@H](N…`
ZINC38192472	1.000	381.4 Da LogP -2.06 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@@H](N)CC[C@@H](…`
ZINC4217451	1.000	381.4 Da LogP -2.06 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@@H](N)CC[C@H](N…`
ZINC5842977	1.000	202.2 Da LogP 2.24 TPSA 63.6	✓ Ro5	✓ Clean	`O=c1ccc2c(O)c3ccoc3cc2o1`
ZINC67665197	1.000	349.3 Da LogP -0.96 TPSA 130.1	✓ Ro5	Alert	`COC1=C(C)C(=O)C2=C(C1=O)[C@H](COC(N)=O)[C@@]1(O…`
ZINC968077	1.000	268.3 Da LogP 3.17 TPSA 59.7	✓ Ro5	✓ Clean	`COc1ccc2c(=O)c(-c3ccc(O)cc3)coc2c1`
ZINC5273895	0.917	257.3 Da LogP -2.04 TPSA 127.1	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC(CO)(CO)CO`
ZINC239229132	0.857	811.9 Da LogP 3.16 TPSA 217.0	2 viol.	Alert	`CC[C@]1(O)C[C@H](O[C@@H]2C[C@H](N(C)C)[C@H](O[C…`
ZINC239229133	0.857	811.9 Da LogP 3.16 TPSA 217.0	2 viol.	Alert	`CC[C@]1(O)C[C@H](O[C@@H]2C[C@H](N(C)C)[C@H](O[C…`
ZINC239229134	0.857	811.9 Da LogP 3.16 TPSA 217.0	2 viol.	Alert	`CC[C@]1(O)C[C@H](O[C@@H]2C[C@H](N(C)C)[C@H](O[C…`
ZINC57588	0.842	282.3 Da LogP 3.48 TPSA 48.7	✓ Ro5	✓ Clean	`COc1ccc(-c2coc3cc(OC)ccc3c2=O)cc1`
ZINC100006731	0.800	334.3 Da LogP -1.65 TPSA 146.9	✓ Ro5	Alert	`CO[C@@]12[C@H]3N[C@@H]3CN1C1=C(C(=O)C(N)=C(C)C1…`
ZINC100028800	0.800	334.3 Da LogP -1.65 TPSA 146.9	✓ Ro5	Alert	`CO[C@@]12[C@H](COC(N)=O)C3=C(C(=O)C(C)=C(N)C3=O…`
ZINC102207625	0.800	334.3 Da LogP -1.65 TPSA 146.9	✓ Ro5	Alert	`CO[C@]12[C@H](COC(N)=O)C3=C(C(=O)C(C)=C(N)C3=O)…`
ZINC102307326	0.800	334.3 Da LogP -1.65 TPSA 146.9	✓ Ro5	Alert	`CO[C@]12[C@H](COC(N)=O)C3=C(C(=O)C(C)=C(N)C3=O)…`
ZINC149479889	0.800	334.3 Da LogP -1.65 TPSA 146.9	✓ Ro5	Alert	`CO[C@@]12[C@H](COC(N)=O)C3=C(C(=O)C(C)=C(N)C3=O…`
ZINC1530537	0.800	334.3 Da LogP -1.65 TPSA 146.9	✓ Ro5	Alert	`CO[C@@]12[C@H]3N[C@H]3CN1C1=C(C(=O)C(N)=C(C)C1=…`
ZINC1634260	0.800	334.3 Da LogP -1.65 TPSA 146.9	✓ Ro5	Alert	`CO[C@@]12[C@H](COC(N)=O)C3=C(C(=O)C(C)=C(N)C3=O…`
ZINC253618058	0.800	334.3 Da LogP -1.65 TPSA 146.9	✓ Ro5	Alert	`CO[C@]12[C@H](COC(N)=O)C3=C(C(=O)C(C)=C(N)C3=O)…`
ZINC253618059	0.800	334.3 Da LogP -1.65 TPSA 146.9	✓ Ro5	Alert	`CO[C@]12[C@H](COC(N)=O)C3=C(C(=O)C(C)=C(N)C3=O)…`
ZINC30726187	0.800	334.3 Da LogP -1.65 TPSA 146.9	✓ Ro5	Alert	`CO[C@@]12[C@H](COC(N)=O)C3=C(C(=O)C(C)=C(N)C3=O…`
ZINC2576403	0.767	282.3 Da LogP 3.56 TPSA 59.7	✓ Ro5	✓ Clean	`CCOc1ccc2c(=O)c(-c3ccc(O)cc3)coc2c1`
ZINC178220	0.762	331.2 Da LogP 4.23 TPSA 39.4	✓ Ro5	✓ Clean	`COc1ccc2c(=O)c(-c3ccc(Br)cc3)coc2c1`
ZINC307961	0.762	270.3 Da LogP 3.61 TPSA 39.4	✓ Ro5	✓ Clean	`COc1ccc2c(=O)c(-c3ccc(F)cc3)coc2c1`
ZINC521218	0.762	286.7 Da LogP 4.12 TPSA 39.4	✓ Ro5	✓ Clean	`COc1ccc2c(=O)c(-c3ccc(Cl)cc3)coc2c1`
ZINC1530141	0.760	229.3 Da LogP -2.82 TPSA 127.1	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC(CO)(CO)CO`
ZINC536953409	0.759	249.7 Da LogP 3.62 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(-c2ccc(O)c(Cl)c2)cc1`
ZINC46554	0.756	252.3 Da LogP 3.47 TPSA 39.4	✓ Ro5	✓ Clean	`COc1ccc2c(=O)c(-c3ccccc3)coc2c1`
ZINC101254165	0.746	388.4 Da LogP -0.51 TPSA 124.1	✓ Ro5	Alert	`CO[C@@]12[C@H](COC(N)=O)C3=C(C(=O)C(C)=C(N4CCCC…`
ZINC95856364	0.746	388.4 Da LogP -0.51 TPSA 124.1	✓ Ro5	Alert	`CO[C@@]12[C@H](COC(N)=O)C3=C(C(=O)C(C)=C(N4CCCC…`
ZINC13522400	0.737	400.4 Da LogP -2.42 TPSA 199.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[S@](=O)CC[C@H](N)…`
ZINC13522403	0.737	400.4 Da LogP -2.42 TPSA 199.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[S@@](=O)CC[C@H](N…`
ZINC13522378	0.732	370.4 Da LogP -1.83 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSC[C@H](N)C(=O)O)[…`
ZINC13522407	0.732	370.4 Da LogP -1.83 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSC[C@H](N)C(=O)O)[…`
ZINC256828117	0.732	370.4 Da LogP -1.83 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSC[C@H](N)C(=O)O)[…`
ZINC256828118	0.732	370.4 Da LogP -1.83 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSC[C@H](N)C(=O)O)[…`
ZINC491070	0.727	310.3 Da LogP 3.39 TPSA 65.7	✓ Ro5	✓ Clean	`COc1ccc(-c2coc3cc(OC(C)=O)ccc3c2=O)cc1`
ZINC1775937521	0.726	423.5 Da LogP -1.02 TPSA 194.7	2 viol.	✓ Clean	`CCCN[C@H](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc…`
ZINC95921230	0.726	423.5 Da LogP -1.02 TPSA 194.7	2 viol.	✓ Clean	`CCCN[C@@H](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cn…`
ZINC13509104	0.724	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCC[C@@H](N)C(=O)O…`
ZINC1532516	0.724	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CSCC[C@H](N)C(=O)O)…`
ZINC33821012	0.724	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCC[C@H](N)C(=O)O)…`
ZINC33821013	0.724	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCC[C@H](N)C(=O)O)…`
ZINC45789230	0.724	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CSCC[C@H](N)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.