Protein profile

KP13_01119

Octaprenyl-diphosphate synthase

Genome: KpKP13

Gene: ispB AHE42487.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H3J7

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Amino acids 323

Annotations 1

Features 15

PDB binders 8

Druggability 0.903

Overview

Basic information about this protein and its source genome.

Accession: KP13_01119
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: ispB AHE42487.1
Status: annotated
Amino acids: 323
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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 30.96
Human E-value: 8.67e-42
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 92.547
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 92.74

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 0.903

Structure A0A0H3H3J7

Pocket Pocket 8

P2Rank 0.924

Structure A0A0H3H3J7

Pocket Pocket 1

ColabFold model

FPocket 0.585 · Pocket 3

P2Rank 0.922 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 187 / 4744 genomes with a hit

Normalized 0.039

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records

Show feature table

Start	End	DB	Term	Name
6	322	SUPERFAMILY	SSF48576	Terpenoid synthases
6	322	InterPro	IPR008949	Isoprenoid synthase domain superfamily
1	323	Gene3D	G3DSA:1.10.600.10	Farnesyl Diphosphate Synthase
1	323	InterPro	IPR008949	Isoprenoid synthase domain superfamily
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
4	321	PANTHER	PTHR12001	GERANYLGERANYL PYROPHOSPHATE SYNTHASE
30	263	Pfam	PF00348	Polyprenyl synthetase
30	263	InterPro	IPR000092	Polyprenyl synthetase
27	321	CDD	cd00685	Trans_IPPS_HT
27	321	InterPro	IPR000092	Polyprenyl synthetase
39	321	SFLD	SFLDS00005	Isoprenoid Synthase Type I
1	323	FunFam	G3DSA:1.10.600.10:FF:000002	Octaprenyl diphosphate synthase

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_A0A0H3H3J7	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01119	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
8				0.903

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	20.5	0.856
2	2.75	0.084
3	1.59	0.025
4	1.59	0.025

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
3				0.585

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	17.29	0.8
2	4.35	0.181
3	2.42	0.065
4	1.58	0.024
5	0.79	0.002

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
2DE	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	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	3Q2Q	Q8NT37	246.1 Da LogP 1.18 TPSA 113.3	✓ Ro5	✓ Clean	`CC(=CCO[P@@](=O)(O)OP(=O)(O)O)C`
FPP	3AQ0	Q5HZ00	382.3 Da LogP 4.63 TPSA 113.3	✓ Ro5	✓ Clean	`CC(=CCC/C(=C/CC/C(=C/CO[P@@](=O)(O)OP(=O)(O)O)/…`
HJX	5ZE6	P0AD57	350.5 Da LogP 6.17 TPSA 66.8	1 viol.	✓ Clean	`CCCCCCCCCCCCCCOc1cccc(c1C(=O)O)O`
ISY	3AQ0	Q5HZ00	262.2 Da LogP 1.90 TPSA 104.1	✓ Ro5	✓ Clean	`CC(=C)CCS[P@@](=O)(O)OP(=O)(O)O`
POP	3OYR	Q9A6I1	176.0 Da LogP -2.08 TPSA 129.9	✓ Ro5	✓ Clean	`O[P@@](=O)([O-])O[P@@](=O)(O)[O-]`
PPV	3AQ0	Q5HZ00	178.0 Da LogP -0.81 TPSA 124.3	✓ Ro5	✓ Clean	`OP(=O)(O)OP(=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	Q964Q8	6.60	317.3 Da LogP 1.62 TPSA 127.1	✓ Ro5	✓ Clean	`CCCCCCCCNCC(P(=O)(O)O)P(=O)(O)O`
CHEMBL407221	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	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	1.000	448.3 Da LogP 3.80 TPSA 148.4	✓ Ro5	✓ Clean	`O=P(O)(O)C(O)(Cc1cccc(-c2cccc3c2oc2ccccc23)c1)P…`
ZINC36176055	1.000	303.2 Da LogP 1.23 TPSA 127.1	✓ Ro5	✓ Clean	`CCCCCCCNCC(P(=O)(O)O)P(=O)(O)O`
ZINC8215740	1.000	246.1 Da LogP 1.18 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCO[P@@](=O)(O)OP(=O)(O)O`
ZINC71769106	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`
ZINC8215849	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	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`
ZINC12494625	0.697	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	0.697	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	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	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	0.641	212.2 Da LogP 2.70 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCOc1cccc(F)c1C(=O)O`
ZINC11958423	0.632	222.3 Da LogP 3.34 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCCOc1ccccc1C(=O)O`
ZINC59030357	0.632	250.3 Da LogP 4.12 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCCCCOc1ccccc1C(=O)O`
ZINC7261547	0.605	208.3 Da LogP 2.95 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCOc1ccccc1C(=O)O`
ZINC16051959	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	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	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	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	0.564	244.2 Da LogP 2.67 TPSA 66.8	✓ Ro5	✓ Clean	`O=C(O)c1c(O)cccc1OCc1ccccc1`
ZINC2530984	0.556	210.2 Da LogP 2.18 TPSA 55.8	✓ Ro5	✓ Clean	`CCOc1cccc(OCC)c1C(=O)O`
ZINC58563493	0.553	326.4 Da LogP 4.83 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCOc1ccc(/C=C\c2cccc(O)c2C(=O)O)cc1`
ZINC20516945	0.550	220.3 Da LogP 3.85 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCOc1ccccc1C(C)=O`
ZINC59087957	0.550	234.3 Da LogP 4.24 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCOc1ccccc1C(C)=O`
ZINC100667816	0.548	229.4 Da LogP 3.49 TPSA 32.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCNC[C@H](C)O`
ZINC2310427	0.548	264.3 Da LogP 2.73 TPSA 61.4	✓ Ro5	✓ Clean	`CCCCCNCP(=O)(O)CNCCCCC`
ZINC2532336	0.548	229.4 Da LogP 3.49 TPSA 32.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCNC[C@@H](C)O`
ZINC73371939	0.548	257.5 Da LogP 4.27 TPSA 32.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCNC[C@@H](C)O`
ZINC73371941	0.548	257.5 Da LogP 4.27 TPSA 32.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCNC[C@H](C)O`
ZINC106400342	0.537	250.3 Da LogP 4.12 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCCCCOc1cccc(C(=O)O)c1`
ZINC1542919	0.537	221.3 Da LogP 2.74 TPSA 52.3	✓ Ro5	✓ Clean	`CCCCCCOc1ccccc1C(N)=O`
ZINC2163669	0.537	278.4 Da LogP 4.90 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCCCCCCOc1cccc(C(=O)O)c1`
ZINC196693230	0.526	236.3 Da LogP 3.47 TPSA 35.5	✓ Ro5	✓ Clean	`CCCOc1cccc(OCCC)c1C(C)=O`
ZINC2029547	0.525	206.3 Da LogP 3.46 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCOc1ccccc1C(C)=O`
ZINC2144825	0.524	224.3 Da LogP 2.01 TPSA 55.8	✓ Ro5	✓ Clean	`CCOCCOc1cccc(O)c1C(C)=O`
ZINC2167300	0.524	263.4 Da LogP 4.38 TPSA 38.3	✓ Ro5	✓ Clean	`CCCCCCCCOc1ccccc1NC(C)=O`
ZINC3220773	0.524	252.3 Da LogP 3.35 TPSA 55.8	✓ Ro5	✓ Clean	`CCCCCCOc1ccc(C(=O)O)cc1OC`
ZINC45329451	0.524	264.4 Da LogP 4.21 TPSA 35.5	✓ Ro5	✓ Clean	`CCCCCCCCOc1ccccc1C(=O)OC`
ZINC5792424	0.524	236.3 Da LogP 3.43 TPSA 35.5	✓ Ro5	✓ Clean	`CCCCCCOc1ccccc1C(=O)OC`
ZINC1603333	0.516	265.3 Da LogP 3.59 TPSA 69.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNP(=O)(O)O`
ZINC100311032	0.515	259.4 Da LogP 2.85 TPSA 52.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC[C@H](O)CO`
ZINC100311035	0.515	259.4 Da LogP 2.85 TPSA 52.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC[C@@H](O)CO`
ZINC16052649	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	0.514	272.4 Da LogP 2.91 TPSA 75.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC[C@H](N)C(=O)O`
ZINC11798718	0.512	208.3 Da LogP 2.95 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCOc1cccc(C(=O)O)c1`
ZINC42393684	0.512	222.3 Da LogP 3.26 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCOc1cc(C(=O)O)ccc1C`
ZINC11953215	0.512	301.2 Da LogP 4.11 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCCOc1ccc(Br)cc1C(=O)O`
ZINC1975391927	0.512	258.3 Da LogP 3.62 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCCOc1ccc(C(=O)O)c(F)c1F`
ZINC2049133	0.512	286.3 Da LogP 4.40 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCCCCOc1ccc(C(=O)O)c(F)c1F`
ZINC526059742	0.512	256.3 Da LogP 3.22 TPSA 46.5	✓ Ro5	✓ Clean	`CC(=O)c1c(O)cccc1OCCc1ccccc1`
ZINC95739849	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.