Protein target profile

PA4569

octaprenyl-diphosphate synthase

Genome: NC_002516.2

Gene: ispB PA4569 3D evidence: AlphaFold DB model UniProt Q9HVL5

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Length 322

Pocket druggability 0.71

Ligand records 58

EC / GO 1 / 4

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: PA4569
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: ispB PA4569
Status: annotated
Amino acids: 322
3D evidence: AlphaFold DB model

2.5.1.90

GO:0106350 Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate = 5 diphosphate + all-trans-octaprenyl diphosphate. GO:0046872 Binding to a metal ion. GO:0004659 Catalysis of the transfer of a prenyl group from one compound (donor) to another (acceptor). GO:0008299 The chemical reactions and pathways resulting in the formation of an isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.

Target profile

Computed evidence for target prioritization.

Human off-target: Hit
Human identity (%): 29.787
Human E-value: 2.94e-09
Gut microbiome off-target: Hit
Essential (DEG): Y
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 0.71

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MQPQAFYRVVAEDFTAVDGIIRRQLTSRVPLVEKIGDYIISAGGKRLRPLLVLLAGKTLGYKGDDLCLLAATIEFLHTSTLLHDDVVDASGLRRGRSTANALWGNAPSVLVGDFLYARSFEMMVELGSMPVMRIISQATRVIAEGEVLQLSKVRDASTTEETYMEVIRGKTAMLFEASTHSAAALCQAGEEQSEALRRFGDYLGIAFQLVDDLLDYRGDAATLGKNVGDDLAEGKPTLPLIVTMRDGTEEQAALVRKAIQQGGSQDLESVCAAVEAAGALDYTANLARDYAARAIACLDTLPDNEYRSALVELSEFAVARTH

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

2.5.1.90

Gene Ontology (GO)

GO:0106350 Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate = 5 diphosphate + all-trans-octaprenyl diphosphate.
GO:0046872 Binding to a metal ion.
GO:0004659 Catalysis of the transfer of a prenyl group from one compound (donor) to another (acceptor).
GO:0008299 The chemical reactions and pathways resulting in the formation of an isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records

Show feature table

Start	End	DB	Term	Name
1	322	FunFam	G3DSA:1.10.600.10:FF:000002	Octaprenyl diphosphate synthase
31	270	Pfam	PF00348	Polyprenyl synthetase
31	270	InterPro	IPR000092	Polyprenyl synthetase
5	321	SUPERFAMILY	SSF48576	Terpenoid synthases
5	321	InterPro	IPR008949	Isoprenoid synthase domain superfamily
37	320	SFLD	SFLDS00005	Isoprenoid Synthase Type I
1	321	Gene3D	G3DSA:1.10.600.10	Farnesyl Diphosphate Synthase
1	321	InterPro	IPR008949	Isoprenoid synthase domain superfamily
5	320	PANTHER	PTHR12001	GERANYLGERANYL PYROPHOSPHATE SYNTHASE
27	320	CDD	cd00685	Trans_IPPS_HT
27	320	InterPro	IPR000092	Polyprenyl synthetase
81	95	ProSitePatterns	PS00723	Polyprenyl synthases signature 1.
81	95	InterPro	IPR033749	Polyprenyl synthetase, conserved site
203	215	ProSitePatterns	PS00444	Polyprenyl synthases signature 2.
203	215	InterPro	IPR033749	Polyprenyl synthetase, 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.

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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 PA4569	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 #3

0.71

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Site 2 FPocket #2

0.415

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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.

58 records

Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 58 via homologs

Structural ligands 5 0 loaded crystals

Bioactive compounds 3 50 ZINC proposed compounds

Drug-like & clean 56 0 PAINS alerts

Best available ligand signal

2DE PDB via homolog 368.3 Da · LogP 4.24 · TPSA 113.3 Open detail RCSB PDB

Detail RCSB PDB 2DE PDB via homolog

Detail RCSB PDB B29 PDB via homolog

Detail RCSB PDB DMA PDB via homolog

Detail RCSB PDB HJX 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
2DE RCSB PDB	3AQC	O66129	368.3 Da LogP 4.24 TPSA 113.3	✓ Ro5	✓ Clean	`CC(=CCC/C(=C/CC/C=C/CO[P@](=O)(O)OP(=O)(O)O)/C)C`
B29 RCSB PDB	5ZLF	P0AD57	448.3 Da LogP 3.80 TPSA 148.4	✓ Ro5	✓ Clean	`c1ccc2c(c1)c3cccc(c3o2)c4cccc(c4)CC(O)(P(=O)(O)…`
DMA RCSB PDB	3Q2Q	Q8NT37	246.1 Da LogP 1.18 TPSA 113.3	✓ Ro5	✓ Clean	`CC(=CCO[P@@](=O)(O)OP(=O)(O)O)C`
HJX RCSB PDB	5ZE6	P0AD57	350.5 Da LogP 6.17 TPSA 66.8	1 viol.	✓ Clean	`CCCCCCCCCCCCCCOc1cccc(c1C(=O)O)O`
POP RCSB PDB	3OYR	Q9A6I1	176.0 Da LogP -2.08 TPSA 129.9	✓ Ro5	✓ Clean	`O[P@@](=O)([O-])O[P@@](=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
CHEMBL260601 ChEMBL	Q964Q8	6.60	317.3 Da LogP 1.62 TPSA 127.1	✓ Ro5	✓ Clean	`CCCCCCCCNCC(P(=O)(O)O)P(=O)(O)O`
CHEMBL407221 ChEMBL	Q964Q8	6.12	247.1 Da LogP -0.33 TPSA 127.1	✓ Ro5	✓ Clean	`CC(C)NCC(P(=O)(O)O)P(=O)(O)O`
FCN ChEMBL	P0AD57	—	138.1 Da LogP -0.09 TPSA 70.1	✓ Ro5	✓ Clean	`C[C@H]1[C@H](O1)P(=O)(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
ZINC16051958 ZINC	1.000	448.3 Da LogP 3.80 TPSA 148.4	✓ Ro5	✓ Clean	`O=P(O)(O)C(O)(Cc1cccc(-c2cccc3c2oc2ccccc23)c1)P…`
ZINC36176055 ZINC	1.000	303.2 Da LogP 1.23 TPSA 127.1	✓ Ro5	✓ Clean	`CCCCCCCNCC(P(=O)(O)O)P(=O)(O)O`
ZINC8215740 ZINC	1.000	246.1 Da LogP 1.18 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCO[P@@](=O)(O)OP(=O)(O)O`
ZINC71769106 ZINC	0.923	326.1 Da LogP 1.30 TPSA 159.8	✓ Ro5	✓ Clean	`CC(C)=CCO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O`
ZINC12494625 ZINC	0.789	382.3 Da LogP 4.63 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CC/C(C)=C/CO[P@@](=O)(O)OP(=O)…`
ZINC8215849 ZINC	0.719	314.2 Da LogP 2.91 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CO[P@@](=O)(O)OP(=O)(O)O`
ZINC8436838 ZINC	0.700	262.1 Da LogP 0.15 TPSA 133.5	✓ Ro5	✓ Clean	`C/C(=C\CO[P@@](=O)(O)OP(=O)(O)O)CO`
ZINC2356589248 ZINC	0.697	382.3 Da LogP 4.63 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCCC(C)=CCCC(C)=CCO[P@](=O)(O)OP(=O)(O)O`
ZINC34661063 ZINC	0.676	394.2 Da LogP 3.02 TPSA 159.8	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CO[P@@](=O)(O)O[P@@](=O)(O)OP(…`
ZINC8218174 ZINC	0.657	462.3 Da LogP 4.75 TPSA 159.8	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CC/C(C)=C/CO[P@@](=O)(O)O[P@@]…`
ZINC86477899 ZINC	0.641	212.2 Da LogP 2.70 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCOc1cccc(F)c1C(=O)O`
ZINC11958423 ZINC	0.632	222.3 Da LogP 3.34 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCCOc1ccccc1C(=O)O`
ZINC59030357 ZINC	0.632	250.3 Da LogP 4.12 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCCCCOc1ccccc1C(=O)O`
ZINC7261547 ZINC	0.605	208.3 Da LogP 2.95 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCOc1ccccc1C(=O)O`
ZINC16051959 ZINC	0.574	434.3 Da LogP 3.56 TPSA 135.3	✓ Ro5	✓ Clean	`O=P(O)(O)C(O)(Cc1cccc(-c2cccc(-c3ccccc3)c2)c1)P…`
ZINC16051960 ZINC	0.574	434.3 Da LogP 3.56 TPSA 135.3	✓ Ro5	✓ Clean	`O=P(O)(O)C(O)(Cc1cccc(-c2ccc(-c3ccccc3)cc2)c1)P…`
ZINC13539354 ZINC	0.571	332.2 Da LogP 3.20 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C(\F)CO[P@](=O)(O)OP(=O)(O)O`
ZINC20502776 ZINC	0.565	393.1 Da LogP -2.06 TPSA 242.1	1 viol.	✓ Clean	`O=P(O)(O)C(CNCC(P(=O)(O)O)P(=O)(O)O)P(=O)(O)O`
ZINC39250619 ZINC	0.564	244.2 Da LogP 2.67 TPSA 66.8	✓ Ro5	✓ Clean	`O=C(O)c1c(O)cccc1OCc1ccccc1`
ZINC2530984 ZINC	0.556	210.2 Da LogP 2.18 TPSA 55.8	✓ Ro5	✓ Clean	`CCOc1cccc(OCC)c1C(=O)O`
ZINC58563493 ZINC	0.553	326.4 Da LogP 4.83 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCOc1ccc(/C=C\c2cccc(O)c2C(=O)O)cc1`
ZINC20516945 ZINC	0.550	220.3 Da LogP 3.85 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCOc1ccccc1C(C)=O`
ZINC59087957 ZINC	0.550	234.3 Da LogP 4.24 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCOc1ccccc1C(C)=O`
ZINC100667816 ZINC	0.548	229.4 Da LogP 3.49 TPSA 32.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCNC[C@H](C)O`
ZINC2310427 ZINC	0.548	264.3 Da LogP 2.73 TPSA 61.4	✓ Ro5	✓ Clean	`CCCCCNCP(=O)(O)CNCCCCC`
ZINC2532336 ZINC	0.548	229.4 Da LogP 3.49 TPSA 32.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCNC[C@@H](C)O`
ZINC73371939 ZINC	0.548	257.5 Da LogP 4.27 TPSA 32.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCNC[C@@H](C)O`
ZINC73371941 ZINC	0.548	257.5 Da LogP 4.27 TPSA 32.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCNC[C@H](C)O`
ZINC106400342 ZINC	0.537	250.3 Da LogP 4.12 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCCCCOc1cccc(C(=O)O)c1`
ZINC1542919 ZINC	0.537	221.3 Da LogP 2.74 TPSA 52.3	✓ Ro5	✓ Clean	`CCCCCCOc1ccccc1C(N)=O`
ZINC2163669 ZINC	0.537	278.4 Da LogP 4.90 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCCCCCCOc1cccc(C(=O)O)c1`
ZINC196693230 ZINC	0.526	236.3 Da LogP 3.47 TPSA 35.5	✓ Ro5	✓ Clean	`CCCOc1cccc(OCCC)c1C(C)=O`
ZINC2029547 ZINC	0.525	206.3 Da LogP 3.46 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCOc1ccccc1C(C)=O`
ZINC2144825 ZINC	0.524	224.3 Da LogP 2.01 TPSA 55.8	✓ Ro5	✓ Clean	`CCOCCOc1cccc(O)c1C(C)=O`
ZINC2167300 ZINC	0.524	263.4 Da LogP 4.38 TPSA 38.3	✓ Ro5	✓ Clean	`CCCCCCCCOc1ccccc1NC(C)=O`
ZINC3220773 ZINC	0.524	252.3 Da LogP 3.35 TPSA 55.8	✓ Ro5	✓ Clean	`CCCCCCOc1ccc(C(=O)O)cc1OC`
ZINC45329451 ZINC	0.524	264.4 Da LogP 4.21 TPSA 35.5	✓ Ro5	✓ Clean	`CCCCCCCCOc1ccccc1C(=O)OC`
ZINC5792424 ZINC	0.524	236.3 Da LogP 3.43 TPSA 35.5	✓ Ro5	✓ Clean	`CCCCCCOc1ccccc1C(=O)OC`
ZINC1603333 ZINC	0.516	265.3 Da LogP 3.59 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNP(=O)(O)O`
ZINC100311032 ZINC	0.515	259.4 Da LogP 2.85 TPSA 52.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC[C@H](O)CO`
ZINC100311035 ZINC	0.515	259.4 Da LogP 2.85 TPSA 52.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC[C@@H](O)CO`
ZINC16052649 ZINC	0.515	419.4 Da LogP 4.87 TPSA 115.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[P+](C)(C)CC(P(=O)(O)O)P(=O)(O)O`
ZINC2383776457 ZINC	0.514	272.4 Da LogP 2.91 TPSA 75.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC[C@H](N)C(=O)O`
ZINC11798718 ZINC	0.512	208.3 Da LogP 2.95 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCOc1cccc(C(=O)O)c1`
ZINC42393684 ZINC	0.512	222.3 Da LogP 3.26 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCOc1cc(C(=O)O)ccc1C`
ZINC11953215 ZINC	0.512	301.2 Da LogP 4.11 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCCOc1ccc(Br)cc1C(=O)O`
ZINC1975391927 ZINC	0.512	258.3 Da LogP 3.62 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCCOc1ccc(C(=O)O)c(F)c1F`
ZINC2049133 ZINC	0.512	286.3 Da LogP 4.40 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCCCCOc1ccc(C(=O)O)c(F)c1F`
ZINC526059742 ZINC	0.512	256.3 Da LogP 3.22 TPSA 46.5	✓ Ro5	✓ Clean	`CC(=O)c1c(O)cccc1OCCc1ccccc1`
ZINC95739849 ZINC	0.512	226.2 Da LogP 3.09 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCOc1cc(F)ccc1C(=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.