Protein profile

KP13_02515

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Genome: KpKP13

Gene: AHE42981.1 ispF Structure source: AlphaFold + ColabFold UniProt A0A0H3GXG5

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Amino acids 159

Annotations 5

Features 16

PDB binders 15

Druggability 0.219

Overview

Basic information about this protein and its source genome.

Accession: KP13_02515
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE42981.1 ispF
Status: annotated
Amino acids: 159
Structure source: AlphaFold + ColabFold

4.6.1.12

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:0008685 Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP. GO:0046872 Binding to a metal ion. GO:0019288 The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 98.113
DEG E-value: 2.26e-112
Localization: Cytoplasmic
ColabFold pLDDT: 96.7

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 0.219

Structure A0A0H3GXG5

Pocket Pocket 4

P2Rank 0.453

Structure A0A0H3GXG5

Pocket Pocket 1

ColabFold model

FPocket 0.256 · Pocket 3

P2Rank 0.596 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 3051 / 4744 genomes with a hit

Normalized 0.643

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

4.6.1.12

Gene Ontology (GO)

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:0008685 Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP.
GO:0046872 Binding to a metal ion.
GO:0019288 The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records

Show feature table

Start	End	DB	Term	Name
1	154	Pfam	PF02542	YgbB family
1	154	InterPro	IPR003526	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
1	156	PANTHER	PTHR43181	2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE, CHLOROPLASTIC
1	156	InterPro	IPR003526	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
1	159	FunFam	G3DSA:3.30.1330.50:FF:000001	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
2	155	NCBIfam	TIGR00151	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
2	155	InterPro	IPR003526	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
2	154	CDD	cd00554	MECDP_synthase
2	154	InterPro	IPR003526	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
1	156	SUPERFAMILY	SSF69765	IpsF-like
1	156	InterPro	IPR036571	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase superfamily
1	156	Hamap	MF_00107	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [ispF].
1	159	Gene3D	G3DSA:3.30.1330.50	-
1	159	InterPro	IPR036571	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase superfamily
35	50	ProSitePatterns	PS01350	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.
35	50	InterPro	IPR020555	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, 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

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_A0A0H3GXG5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02515	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
4				0.219

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				5.45	0.259

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				0.256

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				8.24	0.439

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.

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
1AA	2AMT	P62617	566.4 Da LogP -0.87 TPSA 265.2	3 viol.	✓ Clean	`c1ccc(c(c1)C(=O)OCCO[P@@](=O)(O)O[P@@](=O)(O)OC…`
2AA	2GZL	P62617	679.5 Da LogP -0.11 TPSA 262.3	3 viol.	✓ Clean	`CN(C)c1cccc2c1cccc2S(=O)(=O)NCCO[P@@](=O)(O)O[P…`
6ZB	5L03	A0A069B2G5	219.2 Da LogP 0.54 TPSA 91.1	✓ Ro5	✓ Clean	`c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)NO)N`
C6B	3FBA	P62617	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`C1=CN(C(=O)N=C1N)[C@@H]2[C@@H]([C@@H]([C@@H](O2…`
CAR	3ERN	P62617	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`C1=CN(C(=O)N=C1N)[C@H]2[C@H]([C@@H]([C@H](O2)CO…`
CC7	3ESJ	P62617	305.2 Da LogP -1.40 TPSA 146.1	✓ Ro5	✓ Clean	`C1[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=NC3=O)N)…`
CDI	1JY8	P62617	278.1 Da LogP -0.64 TPSA 142.8	✓ Ro5	✓ Clean	`C[C@@]1([C@@H](CO[P@](=O)(O[P@](=O)(O1)O)O)O)CO`
CDM	1U40	P62617	521.3 Da LogP -3.20 TPSA 273.6	3 viol.	✓ Clean	`C[C@](CO)([C@@H](CO[P@](=O)(O)O[P@](=O)(O)OC[C@…`
CFV	3EOR	P62617	279.2 Da LogP -1.66 TPSA 147.9	✓ Ro5	✓ Clean	`C1=CN(C(=O)N=C1N)C[C@H](CO)OCP(=O)(O)O`
CTN	3T80	Q8ZMF7	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…`
F01	3ELC	P62617	261.2 Da LogP -2.42 TPSA 130.8	✓ Ro5	✓ Clean	`C1=C(C(=NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)CO…`
FPP	1T0A	Q8EBR3	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)/…`
GPP	1YQN	P62617	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`
POP	3GHZ	Q8ZMF7	176.0 Da LogP -2.08 TPSA 129.9	✓ Ro5	✓ Clean	`O[P@@](=O)([O-])O[P@@](=O)(O)[O-]`
SUD	1U43	P62617	601.3 Da LogP -3.08 TPSA 320.1	3 viol.	✓ Clean	`C[C@](CO)([C@@H](CO[P@](=O)(O)O[P@](=O)(O)OC[C@…`

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
CHEMBL3220834	P62617	—	519.3 Da LogP -3.09 TPSA 264.3	3 viol.	✓ Clean	`C[C@](O)(CO)[C@H](O)COP(=O)(O)CP(=O)(O)OC[C@H]1…`

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
ZINC1078621	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=O)n1`
ZINC12336757	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@H](O)[C@@H]2O)c(=O)n1`
ZINC12336758	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@H](CO)[C@H](O)[C@@H]2O)c(=O)n1`
ZINC1530600	1.000	279.2 Da LogP -1.66 TPSA 147.9	✓ Ro5	✓ Clean	`Nc1ccn(C[C@@H](CO)OCP(=O)(O)O)c(=O)n1`
ZINC16969357	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@H](O)[C@H]2O)c(=O)n1`
ZINC2583632	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=O)n1`
ZINC28762983	1.000	279.2 Da LogP -1.66 TPSA 147.9	✓ Ro5	✓ Clean	`Nc1ccn(C[C@H](CO)OCP(=O)(O)O)c(=O)n1`
ZINC3795098	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)c(=O)…`
ZINC3830623	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c(=O)n1`
ZINC3830624	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c(=O)…`
ZINC3978018	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)c(=O)n1`
ZINC6091575	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@H](O)[C@H]2O)c(=O)n1`
ZINC6234828	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@H](CO)[C@H](O)[C@H]2O)c(=O)n1`
ZINC6524892	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO)[C@H](O)[C@H]2O)c(=O)n1`
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`
ZINC895248	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@H](O)[C@@H]2O)c(=O)n1`
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@@]…`
ZINC34085615	0.829	242.2 Da LogP -2.60 TPSA 136.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2N)c(=O)n1`
ZINC13546396	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@H](O)[C@H]2F)c(=O)n1`
ZINC16952044	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@H](O)[C@H]2F)c(=O)n1`
ZINC17174505	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO)[C@@H](O)[C@@H]2F)c(=O…`
ZINC17174506	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2F)c(=O)…`
ZINC2522524	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@H](O)[C@@H]2F)c(=O)n1`
ZINC3817231	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2F)c(=O)n1`
ZINC57331	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO)[C@@H](O)[C@H]2F)c(=O)…`
ZINC5758597	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@@H](O)[C@H]2F)c(=O)n1`
ZINC5758598	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@@H](O)[C@@H]2F)c(=O)…`
ZINC59201305	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@H](O)[C@@H]2F)c(=O)n1`
ZINC6524890	0.786	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@@H](F)[C@H]2O)c(=O)n1`
ZINC85475812	0.786	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@H](F)[C@H]2O)c(=O)n1`
ZINC34307123	0.775	217.3 Da LogP 0.78 TPSA 70.9	✓ Ro5	✓ Clean	`CNC(=O)[C@@H](N)Cc1c[nH]c2ccccc12`
ZINC34482181	0.775	217.3 Da LogP 0.78 TPSA 70.9	✓ Ro5	✓ Clean	`CNC(=O)[C@H](N)Cc1c[nH]c2ccccc12`
ZINC1532829	0.758	234.2 Da LogP 2.79 TPSA 66.8	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/COP(=O)(O)O`
ZINC13546402	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@@H]1[C@@H](O)[C@@H](CO)O[C@H]1n1ccc(N)nc1=O`
ZINC14953681	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@H]1[C@@H](n2ccc(N)nc2=O)O[C@H](CO)[C@H]1O`
ZINC257373216	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@@H]1[C@H](O)[C@H](CO)O[C@H]1n1ccc(N)nc1=O`
ZINC35635704	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@H]1[C@H](O)[C@H](CO)O[C@H]1n1ccc(N)nc1=O`
ZINC38599713	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@H]1[C@@H](O)[C@@H](CO)O[C@H]1n1ccc(N)nc1=O`
ZINC4556822	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@H]1[C@@H](n2ccc(N)nc2=O)O[C@@H](CO)[C@H]1O`
ZINC4556823	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@@H]1[C@@H](n2ccc(N)nc2=O)O[C@@H](CO)[C@H]1O`
ZINC4556824	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@@H]1[C@@H](O)[C@H](CO)O[C@@H]1n1ccc(N)nc1=O`
ZINC4556825	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@H]1[C@@H](O)[C@H](CO)O[C@@H]1n1ccc(N)nc1=O`
ZINC5998209	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1n1ccc(N)nc1=O`
ZINC5998324	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@H]1[C@H](O)[C@@H](CO)O[C@H]1n1ccc(N)nc1=O`
ZINC5541164	0.750	435.4 Da LogP -5.38 TPSA 230.2	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@@H](O[C@H]3O[C@@H](C…`
ZINC5541165	0.750	435.4 Da LogP -5.38 TPSA 230.2	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO)[C@@H](O[C@H]3O[C@@H](…`
ZINC137847133	0.740	439.1 Da LogP -1.43 TPSA 241.0	2 viol.	✓ Clean	`Nc1ccn(C[C@@H](CO)OC[P@@](=O)(O)O[P@@](=O)(O)OP…`

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.