Protein profile

KP13_31942

Farnesyl diphosphate synthase

Genome: KpKP13

Gene: AHE46042.1 ispA Structure source: AlphaFold + ColabFold UniProt A0A0H3GNH4

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Amino acids 299

Annotations 6

Features 17

PDB binders 12

Druggability 0.652

Overview

Basic information about this protein and its source genome.

Accession: KP13_31942
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE46042.1 ispA
Status: annotated
Amino acids: 299
Structure source: AlphaFold + ColabFold

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. 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:0120531 Catalysis of chain elongation of prenyl diphosphate substrates via one or more condensation reactions with isopentenyl diphosphate to generate linear polymers with defined chain lengths. 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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 29.018
Human E-value: 2.5e-12
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 86.622
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 94.88

Selected Druggability evidence

AlphaFold / UniProt model

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 0.652

Structure A0A0H3GNH4

Pocket Pocket 23

P2Rank 0.962

Structure A0A0H3GNH4

Pocket Pocket 1

ColabFold model

FPocket 0.906 · Pocket 1

P2Rank 0.975 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 202 / 4744 genomes with a hit

Normalized 0.043

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

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.
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:0120531 Catalysis of chain elongation of prenyl diphosphate substrates via one or more condensation reactions with isopentenyl diphosphate to generate linear polymers with defined chain lengths.
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.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records

Show feature table

Start	End	DB	Term	Name
1	299	FunFam	G3DSA:1.10.600.10:FF:000001	Geranylgeranyl diphosphate synthase
5	297	SFLD	SFLDS00005	Isoprenoid Synthase Type I
5	297	SFLD	SFLDG01017	Polyprenyl Transferase Like
1	279	SUPERFAMILY	SSF48576	Terpenoid synthases
1	279	InterPro	IPR008949	Isoprenoid synthase domain superfamily
1	298	PANTHER	PTHR43281	FARNESYL DIPHOSPHATE SYNTHASE
29	297	CDD	cd00685	Trans_IPPS_HT
29	297	InterPro	IPR000092	Polyprenyl synthetase
81	97	ProSitePatterns	PS00723	Polyprenyl synthases signature 1.
81	97	InterPro	IPR033749	Polyprenyl synthetase, conserved site
215	227	ProSitePatterns	PS00444	Polyprenyl synthases signature 2.
215	227	InterPro	IPR033749	Polyprenyl synthetase, conserved site
1	299	Gene3D	G3DSA:1.10.600.10	Farnesyl Diphosphate Synthase
1	299	InterPro	IPR008949	Isoprenoid synthase domain superfamily
256	280	Coils	Coil	Coil
32	268	Pfam	PF00348	Polyprenyl synthetase
32	268	InterPro	IPR000092	Polyprenyl synthetase

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

0 + 2

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GNH4	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_31942	ColabFold	—	—	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
9				0.081
16				0.073
7				0.01

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	46.99	0.962
2	3.63	0.109
3	2.21	0.044
4	1.0	0.005

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				0.906
3				0.541

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	38.67	0.96
2	2.46	0.067
3	2.18	0.052
4	0.96	0.005

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.

65 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
6H6	3ZMB	Q9HWY4	207.2 Da LogP 1.07 TPSA 72.4	✓ Ro5	✓ Clean	`c1ccc2c(c1)N(C(=O)O2)CCC(=O)O`
BFQ	4UMJ	Q9HWY4	319.2 Da LogP 0.50 TPSA 138.5	✓ Ro5	✓ Clean	`CCCCC[N@](C)CCC(O)(P(=O)(O)O)P(=O)(O)O`
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	1RQI	P22939	262.2 Da LogP 1.90 TPSA 104.1	✓ Ro5	✓ Clean	`CC(=CCS[P@@](=O)(O)OP(=O)(O)O)C`
GPP	3ZMC	Q9HWY4	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`
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	4LLS	Q16CN9	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`
NVU	3ZL6	Q9HWY4	177.2 Da LogP 1.45 TPSA 63.3	✓ Ro5	✓ Clean	`c1ccc2c(c1)c(no2)CC(=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-]`
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`
ZINC2579357	1.000	248.1 Da LogP 1.26 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)CCO[P@](=O)(O)OP(=O)(O)O`
ZINC374838	0.829	221.2 Da LogP 1.46 TPSA 72.4	✓ Ro5	✓ Clean	`O=C(O)CCCn1c(=O)oc2ccccc21`
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`
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`
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`
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`
ZINC122087	0.632	253.3 Da LogP 2.48 TPSA 52.2	✓ Ro5	✓ Clean	`O=C(Cn1c(=O)oc2ccccc21)c1ccccc1`
ZINC19276177	0.632	206.2 Da LogP 1.33 TPSA 61.2	✓ Ro5	✓ Clean	`NCCCCn1c(=O)oc2ccccc21`
ZINC7862408	0.632	394.4 Da LogP 3.23 TPSA 104.7	✓ Ro5	✓ Clean	`O=C(Cc1noc2ccccc12)OCCCOC(=O)Cc1noc2ccccc12`
ZINC245764	0.628	276.3 Da LogP 0.84 TPSA 64.7	✓ Ro5	✓ Clean	`O=C(CCn1c(=O)oc2ccccc21)N1CCOCC1`
ZINC32738173	0.628	250.3 Da LogP 1.00 TPSA 64.7	✓ Ro5	✓ Clean	`CON(C)C(=O)CCn1c(=O)oc2ccccc21`
ZINC4121512	0.628	290.4 Da LogP 2.63 TPSA 55.5	✓ Ro5	✓ Clean	`CCCN(CCC)C(=O)CCn1c(=O)oc2ccccc21`
ZINC4511978	0.628	298.3 Da LogP 2.33 TPSA 84.5	✓ Ro5	✓ Clean	`O=C(CCn1c(=O)oc2ccccc21)Nc1ccccc1O`
ZINC48480107	0.628	284.3 Da LogP 0.90 TPSA 101.9	✓ Ro5	✓ Clean	`CS(=O)(=O)/N=C(\O)CCn1c(=O)oc2ccccc21`
ZINC58183713	0.628	284.3 Da LogP 0.86 TPSA 103.0	✓ Ro5	✓ Clean	`N#CCN(CC#N)C(=O)CCn1c(=O)oc2ccccc21`
ZINC58186195	0.628	245.2 Da LogP 0.62 TPSA 88.0	✓ Ro5	✓ Clean	`N#CCNC(=O)CCn1c(=O)oc2ccccc21`
ZINC6338424	0.628	296.3 Da LogP 3.01 TPSA 64.2	✓ Ro5	✓ Clean	`O=C(CCCn1c(=O)oc2ccccc21)Nc1ccccc1`
ZINC4121538	0.622	310.4 Da LogP 2.86 TPSA 64.2	✓ Ro5	✓ Clean	`C[C@H](NC(=O)CCn1c(=O)oc2ccccc21)c1ccccc1`

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.