Protein target profile

PA3860

acyl-CoA synthetase

Genome: NC_002516.2

Gene: PA3860 3D evidence: AlphaFold DB model UniProt Q9HXE6

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Length 632

Pocket druggability 0.711

Ligand records 62

EC / GO 0 / 2

Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

4 signals

How to read 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 TPW 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.

Overview

Basic information about this protein and its source genome.

Accession: PA3860
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA3860
Status: annotated
Amino acids: 632
3D evidence: AlphaFold DB model

GO:0016878 Catalysis of the joining of an acid and a thiol via a carbon-sulfur bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. GO:0016405 Catalysis of the reaction: substrate + ATP + CoASH = AMP + diphosphate + substrate-CoA.

Target profile

Computed evidence for target prioritization.

Human off-target: Hit
Human identity (%): 35.366
Human E-value: 6.62e-15
Gut microbiome off-target: Hit
Essential (DEG): N
Localization: Cytoplasmic

Selected pocket evidence

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 0.711

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MNPSPSIAGLSDIEALERVPLEQRDLPSSTYELLQRSARRHGQRIALSCLLHGSAAEEPLRISYAELFARVTQTANALHRLGLESHQAVSFLLPNLPQTHYVIWGGEAAGIVNAINPLLEPEHIAELIRASNTRVLVTLAPFPGTDLWQKVAGLRAQLPELYAIVVVDPANLLPAPQREALKAQRGPLPEGVLDFDTLIADCPADRLESGRAIHPDDVASYFHTGGTTGTPKLAPHSHFNEVAMAEIMGLNADYGVDDVLLCGLPLFHVNGVMVTGLAPFHRGAQVLLAGPQGYRNPTLIQDFWKLVERYRVTSFSGVPTIYAALLQVPSDGRDLSSLRFALCGAAPMPVELIRQFEARTGLKVIEGYGLTEGTCGTSCNPRGGERRPGSIGLRLPYCQVKVAVLDGEGNYLRDAAPNEVGNLCLKGPTVFKGYLQQDRNRDIWIGDGWFNTGDLGRIDEDGYIWLTGRSKDLIIRGGHNIDPQMIEEALHRHPAVALAAAVGKPDAKAGELPVAYIQLKPGASASEEELLEHASRHVPERAAVPKDIWLIESMPVTAVGKTFKPALRLDAIRRVLEEESRRIAEDIRVEVVADERHGQLAHLHVPALDERRQAALEELLGGYALNYRLHAV

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

GO:0016878 Catalysis of the joining of an acid and a thiol via a carbon-sulfur bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
GO:0016405 Catalysis of the reaction: substrate + ATP + CoASH = AMP + diphosphate + substrate-CoA.

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records

Show feature table

Start	End	DB	Term	Name
471	574	Gene3D	G3DSA:3.30.300.30	-
471	574	InterPro	IPR045851	AMP-binding enzyme, C-terminal domain superfamily
486	561	Pfam	PF13193	AMP-binding enzyme C-terminal domain
486	561	InterPro	IPR025110	AMP-binding enzyme, C-terminal domain
34	476	Pfam	PF00501	AMP-binding enzyme
34	476	InterPro	IPR000873	AMP-dependent synthetase/ligase domain
22	570	SUPERFAMILY	SSF56801	Acetyl-CoA synthetase-like
25	572	PANTHER	PTHR43767	LONG-CHAIN-FATTY-ACID--COA LIGASE
23	469	Gene3D	G3DSA:3.40.50.12780	-
23	469	InterPro	IPR042099	ANL, N-terminal domain
215	574	CDD	cd05944	FACL_like_4
221	232	ProSitePatterns	PS00455	Putative AMP-binding domain signature.
221	232	InterPro	IPR020845	AMP-binding, conserved site

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.

Loading 3D structure...

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Structural evidence

0 + 1

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 PA3860	AlphaFold DB	—	—	full sequence	—	Viewing

Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #1

0.711

Show in viewer

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.

62 records

Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 62 via homologs

Structural ligands 8 0 loaded crystals

Bioactive compounds 4 50 ZINC proposed compounds

Drug-like & clean 45 1 PAINS alerts

Best available ligand signal

3UK PDB via homolog 466.3 Da · LogP -0.42 · TPSA 218.2 Open detail RCSB PDB

Detail RCSB PDB 3UK PDB via homolog

Detail RCSB PDB 4UU PDB via homolog

Detail RCSB PDB 4UV PDB via homolog

Detail RCSB PDB 4UW PDB via homolog

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
3UK RCSB PDB	4WV3	F3Y661	466.3 Da LogP -0.42 TPSA 218.2	1 viol.	✓ Clean	`c1ccc(c(c1)C(=O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([…`
4UU RCSB PDB	5BST	O24146	493.4 Da LogP -0.30 TPSA 209.2	1 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
4UV RCSB PDB	5BSU	O24146	507.4 Da LogP -1.12 TPSA 226.3	2 viol.	Alert	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
4UW RCSB PDB	5BSV	O24146	523.4 Da LogP -0.33 TPSA 218.4	2 viol.	✓ Clean	`COC1=CC(=CCC1=O)/C=C/C(=O)OP(=O)(O)OC[C@@H]2[C@…`
JSA RCSB PDB	5ZRN	P9WQ37	530.6 Da LogP 1.12 TPSA 194.9	2 viol.	✓ Clean	`CCCCCCCCCCC[C@H](NS(=O)(=O)OC[C@@H]1[C@H]([C@H]…`
MLI RCSB PDB	3R44	P9WQ37	102.0 Da LogP -3.12 TPSA 80.3	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(=O)[O-]`
OXD RCSB PDB	5IE3	Q9SMT7	90.0 Da LogP -0.84 TPSA 74.6	✓ Ro5	✓ Clean	`C(=O)(C(=O)O)O`
SRT RCSB PDB	5IE0	Q9SMT7	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@H]([C@H](C(=O)O)O)(C(=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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL1315633 ChEMBL	Q94696	—	365.2 Da LogP -2.69 TPSA 217.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
CHEMBL1326967 ChEMBL	Q94696	—	226.3 Da LogP 3.55 TPSA 38.9	✓ Ro5	✓ Clean	`Nc1ccc2nc(-c3ccccc3)sc2c1`
CHEMBL1375740 ChEMBL	Q94696	—	255.3 Da LogP 2.95 TPSA 57.8	✓ Ro5	✓ Clean	`O=C(Nc1nc2ccccc2[nH]1)c1ccccc1F`
CHEMBL3392220 ChEMBL	Q94696	—	448.4 Da LogP -0.51 TPSA 189.3	1 viol.	✓ Clean	`CCN(CC)CC.Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=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
ZINC361067 ZINC	1.000	226.3 Da LogP 3.55 TPSA 38.9	✓ Ro5	✓ Clean	`Nc1ccc2nc(-c3ccccc3)sc2c1`
ZINC225954 ZINC	0.806	241.3 Da LogP 3.13 TPSA 64.9	✓ Ro5	✓ Clean	`Nc1ccc(-c2nc3ccc(N)cc3s2)cc1`
ZINC235533 ZINC	0.788	241.3 Da LogP 3.13 TPSA 64.9	✓ Ro5	✓ Clean	`Nc1cccc(-c2nc3ccc(N)cc3s2)c1`
ZINC8345430 ZINC	0.750	312.3 Da LogP 2.07 TPSA 86.9	✓ Ro5	✓ Clean	`O=C(CNC(=O)c1ccccc1F)Nc1nc2ccccc2[nH]1`
ZINC381794 ZINC	0.744	253.3 Da LogP 2.52 TPSA 78.0	✓ Ro5	✓ Clean	`O=C(Nc1nc2ccccc2[nH]1)c1ccccc1O`
ZINC405324 ZINC	0.744	271.7 Da LogP 3.47 TPSA 57.8	✓ Ro5	✓ Clean	`O=C(Nc1nc2ccccc2[nH]1)c1ccccc1Cl`
ZINC4538149 ZINC	0.735	227.3 Da LogP 2.94 TPSA 51.8	✓ Ro5	✓ Clean	`Nc1ccc2nc(-c3ccncc3)sc2c1`
ZINC31539924 ZINC	0.729	494.4 Da LogP -0.74 TPSA 218.2	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OC(=O…`
ZINC6653557 ZINC	0.721	309.2 Da LogP 3.37 TPSA 57.8	✓ Ro5	✓ Clean	`O=C(Nc1nc2ccccc2[nH]1)c1cc(F)c(F)c(F)c1F`
ZINC235507 ZINC	0.714	242.3 Da LogP 3.25 TPSA 59.1	✓ Ro5	✓ Clean	`Nc1ccc2nc(-c3ccc(O)cc3)sc2c1`
ZINC5589186 ZINC	0.714	260.7 Da LogP 4.20 TPSA 38.9	✓ Ro5	✓ Clean	`Nc1ccc2nc(-c3ccc(Cl)cc3)sc2c1`
ZINC13218513 ZINC	0.707	316.2 Da LogP 3.58 TPSA 57.8	✓ Ro5	✓ Clean	`O=C(Nc1nc2ccccc2[nH]1)c1ccccc1Br`
ZINC441673 ZINC	0.707	251.3 Da LogP 3.12 TPSA 57.8	✓ Ro5	✓ Clean	`Cc1ccccc1C(=O)Nc1nc2ccccc2[nH]1`
ZINC6506834 ZINC	0.707	363.2 Da LogP 3.42 TPSA 57.8	✓ Ro5	✓ Clean	`O=C(Nc1nc2ccccc2[nH]1)c1ccccc1I`
ZINC12589519 ZINC	0.705	307.7 Da LogP 3.75 TPSA 57.8	✓ Ro5	✓ Clean	`O=C(Nc1nc2ccccc2[nH]1)c1cc(F)c(F)cc1Cl`
ZINC4245368 ZINC	0.703	227.3 Da LogP 2.94 TPSA 51.8	✓ Ro5	✓ Clean	`Nc1ccc2nc(-c3cccnc3)sc2c1`
ZINC4245370 ZINC	0.703	242.3 Da LogP 3.25 TPSA 59.1	✓ Ro5	✓ Clean	`Nc1ccc2nc(-c3cccc(O)c3)sc2c1`
ZINC62538947 ZINC	0.703	260.7 Da LogP 4.20 TPSA 38.9	✓ Ro5	✓ Clean	`Nc1ccc2nc(-c3cccc(Cl)c3)sc2c1`
ZINC12546511 ZINC	0.698	305.3 Da LogP 3.83 TPSA 57.8	✓ Ro5	✓ Clean	`O=C(Nc1nc2ccccc2[nH]1)c1ccccc1C(F)(F)F`
ZINC12359024 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC13533920 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC1532740 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC1549593 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC2013424 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC3581021 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC3860635 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)C(=O)O`
ZINC5783661 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC6072527 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC12588992 ZINC	0.690	306.2 Da LogP 4.12 TPSA 57.8	✓ Ro5	✓ Clean	`O=C(Nc1nc2ccccc2[nH]1)c1cccc(Cl)c1Cl`
ZINC13218630 ZINC	0.690	287.3 Da LogP 3.97 TPSA 57.8	✓ Ro5	✓ Clean	`O=C(Nc1nc2ccccc2[nH]1)c1cccc2ccccc12`
ZINC17304201 ZINC	0.689	324.1 Da LogP 4.26 TPSA 57.8	✓ Ro5	✓ Clean	`O=C(Nc1nc2ccccc2[nH]1)c1cc(F)c(Cl)cc1Cl`
ZINC9115469 ZINC	0.681	285.3 Da LogP 2.96 TPSA 67.0	✓ Ro5	✓ Clean	`COc1ccc(C(=O)Nc2nc3ccccc3[nH]2)c(F)c1`
ZINC6589933 ZINC	0.674	341.4 Da LogP 4.05 TPSA 74.8	✓ Ro5	✓ Clean	`O=C(Nc1nc2ccccc2[nH]1)c1ccccc1C(=O)c1ccccc1`
ZINC12544692 ZINC	0.667	330.4 Da LogP 2.19 TPSA 103.9	✓ Ro5	✓ Clean	`CS(=O)(=O)Nc1ccccc1C(=O)Nc1nc2ccccc2[nH]1`
ZINC12538671 ZINC	0.659	306.2 Da LogP 4.12 TPSA 57.8	✓ Ro5	✓ Clean	`O=C(Nc1nc2ccccc2[nH]1)c1cc(Cl)ccc1Cl`
ZINC13228399 ZINC	0.659	265.3 Da LogP 3.43 TPSA 57.8	✓ Ro5	✓ Clean	`Cc1cccc(C(=O)Nc2nc3ccccc3[nH]2)c1C`
ZINC14048562 ZINC	0.659	270.3 Da LogP 2.50 TPSA 70.7	✓ Ro5	✓ Clean	`O=C(Nc1nc2ccccc2[nH]1)c1cccnc1S`
ZINC406618 ZINC	0.659	267.3 Da LogP 2.82 TPSA 67.0	✓ Ro5	✓ Clean	`COc1ccccc1C(=O)Nc1nc2ccccc2[nH]1`
ZINC9910431 ZINC	0.659	273.2 Da LogP 3.09 TPSA 57.8	✓ Ro5	✓ Clean	`O=C(Nc1nc2ccccc2[nH]1)c1ccc(F)c(F)c1`
ZINC1595024 ZINC	0.657	245.7 Da LogP 4.62 TPSA 12.9	✓ Ro5	✓ Clean	`Clc1ccc2nc(-c3ccccc3)sc2c1`
ZINC1682939 ZINC	0.657	229.3 Da LogP 4.10 TPSA 12.9	✓ Ro5	✓ Clean	`Fc1ccc2nc(-c3ccccc3)sc2c1`
ZINC29413288 ZINC	0.657	227.3 Da LogP 3.67 TPSA 33.1	✓ Ro5	✓ Clean	`Oc1ccc2nc(-c3ccccc3)sc2c1`
ZINC402244 ZINC	0.657	225.3 Da LogP 4.27 TPSA 12.9	✓ Ro5	✓ Clean	`Cc1ccc2nc(-c3ccccc3)sc2c1`
ZINC73638544 ZINC	0.657	290.2 Da LogP 4.73 TPSA 12.9	✓ Ro5	✓ Clean	`Brc1ccc2nc(-c3ccccc3)sc2c1`
ZINC12603357 ZINC	0.652	289.7 Da LogP 3.61 TPSA 57.8	✓ Ro5	✓ Clean	`O=C(Nc1nc2ccccc2[nH]1)c1ccc(F)cc1Cl`
ZINC17304200 ZINC	0.652	334.1 Da LogP 3.72 TPSA 57.8	✓ Ro5	✓ Clean	`O=C(Nc1nc2ccccc2[nH]1)c1ccc(F)cc1Br`
ZINC6567101 ZINC	0.652	303.3 Da LogP 3.42 TPSA 67.0	✓ Ro5	✓ Clean	`O=C(Nc1nc2ccccc2[nH]1)c1ccccc1OC(F)F`
ZINC72704 ZINC	0.652	331.4 Da LogP 4.62 TPSA 57.8	✓ Ro5	✓ Clean	`O=C(Nc1ccc(-c2nc3ccccc3[nH]2)cc1)c1ccccc1F`
ZINC6566971 ZINC	0.651	273.2 Da LogP 3.09 TPSA 57.8	✓ Ro5	✓ Clean	`O=C(Nc1nc2ccccc2[nH]1)c1cc(F)cc(F)c1`
ZINC31475423 ZINC	0.649	434.3 Da LogP -2.99 TPSA 238.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@@](=O)(O)OC(=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.