Protein profile

PA4043

geranyltranstransferase

Genome: NC_002516.2

Gene: PA4043 ispA Structure source: Experimental + AlphaFold UniProt Q9HWY4

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Amino acids 295

Annotations 6

Features 16

PDB binders 13

Druggability 0.626

Overview

Basic information about this protein and its source genome.

Accession: PA4043
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA4043 ispA
Status: annotated
Amino acids: 295
Structure source: Experimental + AlphaFold

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. 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:0008654 The chemical reactions and pathways resulting in the formation of a phospholipid, a lipid containing phosphoric acid as a mono- or diester. GO:0016114 The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure. 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 (%): 28.854
Human E-value: 5.72e-13
Gut microbiome off-target: hit
Essential (DEG): Y
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 0.626

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
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:0008654 The chemical reactions and pathways resulting in the formation of a phospholipid, a lipid containing phosphoric acid as a mono- or diester.
GO:0016114 The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure.
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.

16 records

Show feature table

Start	End	DB	Term	Name
29	259	Pfam	PF00348	Polyprenyl synthetase
29	259	InterPro	IPR000092	Polyprenyl synthetase
26	293	CDD	cd00685	Trans_IPPS_HT
26	293	InterPro	IPR000092	Polyprenyl synthetase
1	295	Gene3D	G3DSA:1.10.600.10	Farnesyl Diphosphate Synthase
1	295	InterPro	IPR008949	Isoprenoid synthase domain superfamily
1	295	FunFam	G3DSA:1.10.600.10:FF:000001	Geranylgeranyl diphosphate synthase
5	287	SUPERFAMILY	SSF48576	Terpenoid synthases
5	287	InterPro	IPR008949	Isoprenoid synthase domain superfamily
5	293	SFLD	SFLDG01017	Polyprenyl Transferase Like
5	293	SFLD	SFLDS00005	Isoprenoid Synthase Type I
4	294	PANTHER	PTHR43281	FARNESYL DIPHOSPHATE SYNTHASE
80	96	ProSitePatterns	PS00723	Polyprenyl synthases signature 1.
80	96	InterPro	IPR033749	Polyprenyl synthetase, conserved site
214	226	ProSitePatterns	PS00444	Polyprenyl synthases signature 2.
214	226	InterPro	IPR033749	Polyprenyl synthetase, conserved site

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

6 + 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 3ZCD	X-ray	1.55 Å	A,B	100.0% 1-295	PDBe RCSB PDBj File	Viewing
PDB 3ZOU	X-ray	1.55 Å	A,B	100.0% 1-295	PDBe RCSB PDBj File	Loaded
PDB 3ZL6	X-ray	1.85 Å	A,B	100.0% 1-295	PDBe RCSB PDBj File	Loaded
PDB 4UMJ	X-ray	1.85 Å	A,B	100.0% 1-295	PDBe RCSB PDBj File	Loaded
PDB 3ZMC	X-ray	1.87 Å	A,B	100.0% 1-295	PDBe RCSB PDBj File	Loaded
PDB 3ZMB	X-ray	1.90 Å	A,B	100.0% 1-295	PDBe RCSB PDBj File	Loaded
AlphaFold PA4043	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				0.443

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	15.06	0.744
2	2.01	0.043
3	1.78	0.033
4	1.23	0.011

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				0.36
1				0.313

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.

66 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.

Ligand	Source crystal	MW · LogP · TPSA	Lipinski	PAINS	SMILES
6H6	3ZMB 1.90 Å Open crystal	207.2 Da LogP 1.07 TPSA 72.4	✓ Ro5	✓ Clean	`c1ccc2c(c1)N(C(=O)O2)CCC(=O)O`
BFQ	4UMJ 1.85 Å Open crystal	319.2 Da LogP 0.50 TPSA 138.5	✓ Ro5	✓ Clean	`CCCCC[N@](C)CCC(O)(P(=O)(O)O)P(=O)(O)O`
GPP	3ZMC 1.87 Å Open crystal	314.2 Da LogP 2.91 TPSA 113.3	✓ Ro5	✓ Clean	`CC(=CCC/C(=C/CO[P@@](=O)(O)OP(=O)(O)O)/C)C`
NVU	3ZL6 1.85 Å Open crystal	177.2 Da LogP 1.45 TPSA 63.3	✓ Ro5	✓ Clean	`c1ccc2c(c1)c(no2)CC(=O)O`

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
DMA	3P41	Q4K5A6	246.1 Da LogP 1.18 TPSA 113.3	✓ Ro5	✓ Clean	`CC(=CCO[P@@](=O)(O)OP(=O)(O)O)C`
DPO	1RQI	P22939	173.9 Da LogP -3.34 TPSA 135.6	✓ Ro5	✓ Clean	`[O-]P(=O)([O-])OP(=O)([O-])[O-]`
DST	3KRF	Q9SBR3	262.2 Da LogP 1.90 TPSA 104.1	✓ Ro5	✓ Clean	`CC(=CCS[P@@](=O)(O)OP(=O)(O)O)C`
GST	4LLS	Q16CN9	330.3 Da LogP 3.62 TPSA 104.1	✓ Ro5	✓ Clean	`CC(=CCCC(=CCS[P@](=O)(O)OP(=O)(O)O)C)C`
IPE	3KRC	Q9SBR3	246.1 Da LogP 1.18 TPSA 113.3	✓ Ro5	✓ Clean	`CC(=C)CCO[P@@](=O)(O)OP(=O)(O)O`
IPR	2FOR	A0A0H2UXE9	248.1 Da LogP 1.26 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)CCO[P@@](=O)(O)OP(=O)(O)O`
POP	3P41	Q4K5A6	176.0 Da LogP -2.08 TPSA 129.9	✓ Ro5	✓ Clean	`O[P@@](=O)([O-])O[P@@](=O)(O)[O-]`
PPV	3KRF	Q9SBR3	178.0 Da LogP -0.81 TPSA 124.3	✓ Ro5	✓ Clean	`OP(=O)(O)OP(=O)(O)O`
RIS	1RQJ	P22939	283.1 Da LogP -0.37 TPSA 148.2	✓ Ro5	✓ Clean	`c1cc(cnc1)CC(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
CHEMBL199858	P22939	6.16	322.2 Da LogP 0.04 TPSA 153.1	✓ Ro5	✓ Clean	`O=P(O)(O)C(O)(Cn1cnc2ccccc21)P(=O)(O)O`
CHEMBL573338	P22939	—	562.6 Da LogP 8.16 TPSA 110.1	2 viol.	✓ Clean	`CC(C)=CCC/C(C)=C/CC/C(C)=C/CO[32P](=O)(O)O[32P]…`
FCN	P22939	—	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
ZINC121380	1.000	207.2 Da LogP 1.07 TPSA 72.4	✓ Ro5	✓ Clean	`O=C(O)CCn1c(=O)oc2ccccc21`
ZINC1531009	1.000	283.1 Da LogP -0.37 TPSA 148.2	✓ Ro5	✓ Clean	`O=P(O)(O)C(O)(Cc1cccnc1)P(=O)(O)O`
ZINC1533877	1.000	319.2 Da LogP 0.50 TPSA 138.5	✓ Ro5	✓ Clean	`CCCCCN(C)CCC(O)(P(=O)(O)O)P(=O)(O)O`
ZINC8215849	1.000	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`
ZINC12494625	0.969	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)…`
ZINC2356589248	0.969	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	0.939	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	0.912	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@@]…`
ZINC374838	0.829	221.2 Da LogP 1.46 TPSA 72.4	✓ Ro5	✓ Clean	`O=C(O)CCCn1c(=O)oc2ccccc21`
ZINC1532829	0.758	234.2 Da LogP 2.79 TPSA 66.8	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/COP(=O)(O)O`
ZINC344606	0.750	206.2 Da LogP 0.47 TPSA 78.2	✓ Ro5	✓ Clean	`NC(=O)CCn1c(=O)oc2ccccc21`
ZINC65748698	0.737	311.2 Da LogP 0.67 TPSA 137.2	✓ Ro5	✓ Clean	`CCO[P@](=O)(O)[C@](O)(Cc1cccnc1)P(=O)(O)O`
ZINC65748699	0.737	311.2 Da LogP 0.67 TPSA 137.2	✓ Ro5	✓ Clean	`CCO[P@](=O)(O)[C@@](O)(Cc1cccnc1)P(=O)(O)O`
ZINC2556391	0.735	302.4 Da LogP 4.51 TPSA 66.8	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O)O`
ZINC8215740	0.719	246.1 Da LogP 1.18 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCO[P@@](=O)(O)OP(=O)(O)O`
ZINC36804	0.711	324.3 Da LogP 2.23 TPSA 87.4	✓ Ro5	✓ Clean	`O=C(CCn1c(=O)oc2ccccc21)n1c(=O)oc2ccccc21`
ZINC4328522	0.706	338.4 Da LogP 3.37 TPSA 70.3	✓ Ro5	✓ Clean	`O=c1oc2ccccc2n1CCCCCn1c(=O)oc2ccccc21`
ZINC73723	0.703	223.3 Da LogP 2.44 TPSA 55.4	✓ Ro5	✓ Clean	`O=C(O)CCn1c(=S)oc2ccccc21`
ZINC342375	0.700	282.3 Da LogP 2.62 TPSA 64.2	✓ Ro5	✓ Clean	`O=C(CCn1c(=O)oc2ccccc21)Nc1ccccc1`
ZINC7277184	0.700	283.3 Da LogP 2.59 TPSA 61.4	✓ Ro5	✓ Clean	`O=C(CCn1c(=O)oc2ccccc21)Oc1ccccc1`
ZINC20305771	0.692	221.2 Da LogP 1.16 TPSA 61.4	✓ Ro5	✓ Clean	`COC(=O)CCn1c(=O)oc2ccccc21`
ZINC48355656	0.692	234.3 Da LogP 1.07 TPSA 55.5	✓ Ro5	✓ Clean	`CN(C)C(=O)CCn1c(=O)oc2ccccc21`
ZINC22066894	0.686	375.3 Da LogP 3.12 TPSA 94.5	✓ Ro5	✓ Clean	`CCCCCN(C)CCC(O)(P(=O)(OC)OC)P(=O)(OC)OC`
ZINC71769106	0.676	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`
ZINC11689442	0.676	247.1 Da LogP -0.42 TPSA 128.0	✓ Ro5	✓ Clean	`O=C(O)[C@](O)(Cc1cccnc1)P(=O)(O)O`
ZINC1550478	0.676	247.1 Da LogP -0.42 TPSA 128.0	✓ Ro5	✓ Clean	`O=C(O)[C@@](O)(Cc1cccnc1)P(=O)(O)O`
ZINC6838070	0.676	266.3 Da LogP 2.69 TPSA 55.1	✓ Ro5	✓ Clean	`O=C(Cc1noc2ccccc12)NCc1ccccc1`
ZINC8007169	0.676	252.3 Da LogP 3.01 TPSA 55.1	✓ Ro5	✓ Clean	`O=C(Cc1noc2ccccc12)Nc1ccccc1`
ZINC245801	0.667	296.3 Da LogP 2.65 TPSA 55.5	✓ Ro5	✓ Clean	`CN(C(=O)CCn1c(=O)oc2ccccc21)c1ccccc1`
ZINC383240	0.667	239.3 Da LogP 2.84 TPSA 35.1	✓ Ro5	✓ Clean	`O=c1oc2ccccc2n1CCc1ccccc1`
ZINC4121531	0.667	296.3 Da LogP 2.30 TPSA 64.2	✓ Ro5	✓ Clean	`O=C(CCn1c(=O)oc2ccccc21)NCc1ccccc1`
ZINC24583457	0.659	260.3 Da LogP 1.61 TPSA 55.5	✓ Ro5	✓ Clean	`O=C(CCn1c(=O)oc2ccccc21)N1CCCC1`
ZINC4121511	0.659	262.3 Da LogP 1.85 TPSA 55.5	✓ Ro5	✓ Clean	`CCN(CC)C(=O)CCn1c(=O)oc2ccccc21`
ZINC71404870	0.657	230.3 Da LogP 4.23 TPSA 26.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/COP(C)(C)=O`
ZINC8436838	0.657	262.1 Da LogP 0.15 TPSA 133.5	✓ Ro5	✓ Clean	`C/C(=C\CO[P@@](=O)(O)OP(=O)(O)O)CO`
ZINC7278545	0.651	372.4 Da LogP 3.89 TPSA 64.2	✓ Ro5	✓ Clean	`O=C(CCn1c(=O)oc2ccccc21)NC(c1ccccc1)c1ccccc1`
ZINC153916	0.650	221.2 Da LogP 1.38 TPSA 72.4	✓ Ro5	✓ Clean	`Cc1ccc2oc(=O)n(CCC(=O)O)c2c1`
ZINC245911	0.650	286.1 Da LogP 1.83 TPSA 72.4	✓ Ro5	✓ Clean	`O=C(O)CCn1c(=O)oc2cc(Br)ccc21`
ZINC4218219	0.650	241.6 Da LogP 1.72 TPSA 72.4	✓ Ro5	✓ Clean	`O=C(O)CCn1c(=O)oc2cc(Cl)ccc21`
ZINC6528356	0.650	241.6 Da LogP 1.72 TPSA 72.4	✓ Ro5	✓ Clean	`O=C(O)CCn1c(=O)oc2ccc(Cl)cc21`
ZINC19946295	0.649	227.2 Da LogP 2.61 TPSA 63.3	✓ Ro5	✓ Clean	`O=C(O)Cc1noc2ccc3ccccc3c12`
ZINC52819430	0.644	326.4 Da LogP 1.83 TPSA 84.5	✓ Ro5	✓ Clean	`O=C(CCn1c(=O)oc2ccccc21)NC[C@@H](O)c1ccccc1`
ZINC52819431	0.644	326.4 Da LogP 1.83 TPSA 84.5	✓ Ro5	✓ Clean	`O=C(CCn1c(=O)oc2ccccc21)NC[C@H](O)c1ccccc1`
ZINC4121516	0.643	288.3 Da LogP 2.39 TPSA 55.5	✓ Ro5	✓ Clean	`O=C(CCn1c(=O)oc2ccccc21)N1CCCCCC1`
ZINC4121520	0.643	248.3 Da LogP 1.51 TPSA 64.2	✓ Ro5	✓ Clean	`CC(C)NC(=O)CCn1c(=O)oc2ccccc21`
ZINC2183252	0.641	266.3 Da LogP 3.03 TPSA 46.3	✓ Ro5	✓ Clean	`CN(C(=O)Cc1noc2ccccc12)c1ccccc1`
ZINC245790	0.636	310.4 Da LogP 2.34 TPSA 64.2	✓ Ro5	✓ Clean	`O=C(CCn1c(=O)oc2ccccc21)NCCc1ccccc1`
ZINC245808	0.636	310.4 Da LogP 3.04 TPSA 55.5	✓ Ro5	✓ Clean	`CCN(C(=O)CCn1c(=O)oc2ccccc21)c1ccccc1`
ZINC13539354	0.632	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`
ZINC7862408	0.632	394.4 Da LogP 3.23 TPSA 104.7	✓ Ro5	✓ Clean	`O=C(Cc1noc2ccccc12)OCCCOC(=O)Cc1noc2ccccc12`

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.