Protein profile

PA3633

2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

Genome: NC_002516.2

Gene: ygbP Structure source: ColabFold

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Amino acids 234

Annotations 4

Features 16

PDB binders 7

Druggability 0.288

Overview

Basic information about this protein and its source genome.

Accession: PA3633
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: ygbP
Status: annotated
Amino acids: 234
Structure source: 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:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0070567 Catalysis of the transfer of a cytidylyl group to an acceptor. GO:0050518 Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + CTP = 4-CDP-2-C-methyl-D-erythritol + diphosphate.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 25.221
Human E-value: 1.65e-10
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 0.288

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 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:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
GO:0070567 Catalysis of the transfer of a cytidylyl group to an acceptor.
GO:0050518 Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + CTP = 4-CDP-2-C-methyl-D-erythritol + diphosphate.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records

Show feature table

Start	End	DB	Term	Name
10	230	SUPERFAMILY	SSF53448	Nucleotide-diphospho-sugar transferases
10	230	InterPro	IPR029044	Nucleotide-diphospho-sugar transferases
9	228	CDD	cd02516	CDP-ME_synthetase
9	228	InterPro	IPR034683	Cytidylyltransferase IspD/TarI
10	230	NCBIfam	TIGR00453	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
10	230	InterPro	IPR001228	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
9	231	PANTHER	PTHR32125	2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTIC
11	227	Pfam	PF01128	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
11	227	InterPro	IPR034683	Cytidylyltransferase IspD/TarI
5	233	Gene3D	G3DSA:3.90.550.10	Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
5	233	InterPro	IPR029044	Nucleotide-diphospho-sugar transferases
8	232	Hamap	MF_00108	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase [ispD].
8	232	InterPro	IPR001228	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
108	115	ProSitePatterns	PS01295	4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature.
108	115	InterPro	IPR018294	4-diphosphocytidyl-2C-methyl-D-erythritol synthase, conserved site
7	232	FunFam	G3DSA:3.90.550.10:FF:000003	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

0 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
ColabFold PA3633	ColabFold	—	—	full sequence	—	Viewing

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				0.288

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.

63 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
30A	2YCM	P69834	303.7 Da LogP 2.38 TPSA 87.7	✓ Ro5	✓ Clean	`c1ccc(cc1)Cc2c(nc3c(cnn3c2O)C(=O)O)Cl`
CAD	4ZDQ	Q2SWT6	138.0 Da LogP 0.11 TPSA 37.3	✓ Ro5	✓ Clean	`C[As](=O)(C)O`
CDM	3Q80	P9WKG9	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@…`
DTT	4NAL	P69834	154.3 Da LogP -0.43 TPSA 40.5	✓ Ro5	✓ Clean	`C([C@@H]([C@H](CS)O)O)S`
H70	4NAL	P69834	464.8 Da LogP 5.98 TPSA 36.0	1 viol.	✓ Clean	`c1c(cc(c(c1c2c(c(c([nH]2)Br)Br)Br)O)Cl)Cl`
MW5	2YC3	P69834	260.7 Da LogP 1.66 TPSA 63.1	✓ Ro5	✓ Clean	`c1ccc(cc1)CC2=C(N=C3NC=NN3C2=O)Cl`
V2V	6XHQ	Q2G1C0	537.3 Da LogP -4.23 TPSA 293.8	3 viol.	✓ Clean	`C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H](C(O2)COP(=…`

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
CHEMBL2289489	P69834	7.46	284.7 Da LogP 2.55 TPSA 74.2	✓ Ro5	✓ Clean	`N#Cc1cnn2c(O)c(Cc3ccccc3)c(Cl)nc12`
CHEMBL2289491	P69834	6.85	260.7 Da LogP 2.07 TPSA 63.3	✓ Ro5	✓ Clean	`Oc1c(Cc2ccccc2)c(Cl)nc2ncnn12`
CHEMBL1592555	Q2SWT6	—	273.7 Da LogP 2.63 TPSA 55.6	✓ Ro5	✓ Clean	`Cn1ncc2c(NCc3ccc(Cl)cc3)ncnc21`
CHEMBL3735118	Q2SWT6	—	308.2 Da LogP 3.28 TPSA 55.6	✓ Ro5	✓ Clean	`Cn1ncc2c(NCc3ccc(Cl)c(Cl)c3)ncnc21`
CHEMBL3735997	Q2SWT6	—	269.3 Da LogP 1.72 TPSA 75.9	✓ Ro5	✓ Clean	`Cn1ncc2c(NCCc3ccc(O)cc3)ncnc21`
CHEMBL3736022	Q2SWT6	—	322.2 Da LogP 3.32 TPSA 55.6	✓ Ro5	✓ Clean	`Cn1ncc2c(NCCc3ccc(Cl)cc3Cl)ncnc21`

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
ZINC1577353	1.000	273.7 Da LogP 2.63 TPSA 55.6	✓ Ro5	✓ Clean	`Cn1ncc2c(NCc3ccc(Cl)cc3)ncnc21`
ZINC4338812	0.792	308.2 Da LogP 3.28 TPSA 55.6	✓ Ro5	✓ Clean	`Cn1ncc2c(NCc3ccc(Cl)cc3Cl)ncnc21`
ZINC3356779	0.786	253.3 Da LogP 2.28 TPSA 55.6	✓ Ro5	✓ Clean	`Cc1ccc(CNc2ncnc3c2cnn3C)cc1`
ZINC5730157	0.778	264.3 Da LogP 2.21 TPSA 74.2	✓ Ro5	✓ Clean	`Cc1nc2c(C#N)cnn2c(O)c1Cc1ccccc1`
ZINC9532131	0.778	287.8 Da LogP 2.67 TPSA 55.6	✓ Ro5	✓ Clean	`Cn1ncc2c(NCCc3ccc(Cl)cc3)ncnc21`
ZINC1577357	0.773	253.3 Da LogP 2.02 TPSA 55.6	✓ Ro5	✓ Clean	`Cn1ncc2c(NCCc3ccccc3)ncnc21`
ZINC40493231	0.773	255.3 Da LogP 1.68 TPSA 75.9	✓ Ro5	✓ Clean	`Cn1ncc2c(NCc3ccc(O)cc3)ncnc21`
ZINC8584776	0.767	257.3 Da LogP 2.11 TPSA 55.6	✓ Ro5	✓ Clean	`Cn1ncc2c(NCc3ccc(F)cc3)ncnc21`
ZINC97020230	0.765	366.7 Da LogP 3.43 TPSA 55.6	✓ Ro5	✓ Clean	`Cn1ncc2c(NCCc3cc(Cl)ccc3Br)ncnc21`
ZINC838233	0.762	239.3 Da LogP 1.98 TPSA 55.6	✓ Ro5	✓ Clean	`Cn1ncc2c(NCc3ccccc3)ncnc21`
ZINC8216074	0.754	477.3 Da LogP -2.95 TPSA 253.3	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@](=O)(O)…`
ZINC8551188	0.754	477.3 Da LogP -2.95 TPSA 253.3	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@](=O)(O)O…`
ZINC12502055	0.746	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC13431059	0.746	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC53683723	0.746	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC82142140	0.746	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC8582968	0.745	273.7 Da LogP 2.63 TPSA 55.6	✓ Ro5	✓ Clean	`Cn1ncc2c(NCc3cccc(Cl)c3)ncnc21`
ZINC9532026	0.745	283.3 Da LogP 2.03 TPSA 64.9	✓ Ro5	✓ Clean	`COc1ccc(CCNc2ncnc3c2cnn3C)cc1`
ZINC9532170	0.744	240.3 Da LogP 1.37 TPSA 68.5	✓ Ro5	✓ Clean	`Cn1ncc2c(NCc3ccncc3)ncnc21`
ZINC104864216	0.741	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@](=O)(O)OP(=O)(O)O)[C…`
ZINC12504412	0.741	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC12504413	0.741	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC12504414	0.741	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC13431045	0.741	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC13431047	0.741	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC13548733	0.741	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC33913782	0.741	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC8215624	0.741	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC1577358	0.733	269.3 Da LogP 1.98 TPSA 64.9	✓ Ro5	✓ Clean	`COc1ccc(CNc2ncnc3c2cnn3C)cc1`
ZINC8216134	0.721	446.2 Da LogP -2.35 TPSA 238.9	2 viol.	✓ Clean	`NCCO[P@@](=O)(O)O[P@](=O)(O)OC[C@H]1O[C@@H](n2c…`
ZINC12372230	0.714	240.3 Da LogP 1.73 TPSA 63.3	✓ Ro5	✓ Clean	`Cc1nc2ncnn2c(O)c1Cc1ccccc1`
ZINC42240352	0.708	259.3 Da LogP 2.08 TPSA 55.6	✓ Ro5	✓ Clean	`Cn1ncc2c(NCCc3ccsc3)ncnc21`
ZINC337881621	0.706	307.3 Da LogP 2.44 TPSA 55.6	✓ Ro5	✓ Clean	`Cn1ncc2c(NCCc3ccc(F)c(F)c3F)ncnc21`
ZINC26775664	0.702	297.4 Da LogP 2.51 TPSA 64.9	✓ Ro5	✓ Clean	`CCOCc1ccc(CNc2ncnc3c2cnn3C)cc1`
ZINC52100767	0.702	317.4 Da LogP 1.38 TPSA 89.8	✓ Ro5	✓ Clean	`Cn1ncc2c(NCc3ccc(S(C)(=O)=O)cc3)ncnc21`
ZINC12876870	0.700	297.3 Da LogP 1.75 TPSA 74.1	✓ Ro5	✓ Clean	`Cn1ncc2c(NCc3ccc4c(c3)OCCO4)ncnc21`
ZINC9058175	0.700	332.4 Da LogP 0.67 TPSA 115.8	✓ Ro5	✓ Clean	`Cn1ncc2c(NCCc3ccc(S(N)(=O)=O)cc3)ncnc21`
ZINC14167932	0.694	271.3 Da LogP 2.42 TPSA 55.6	✓ Ro5	✓ Clean	`Cc1ccc(CNc2ncnc3c2cnn3C)cc1F`
ZINC14206747	0.694	299.3 Da LogP 1.99 TPSA 74.1	✓ Ro5	✓ Clean	`COc1ccc(CNc2ncnc3c2cnn3C)cc1OC`
ZINC1718454	0.689	308.2 Da LogP 3.28 TPSA 55.6	✓ Ro5	✓ Clean	`Cn1ncc2c(NCc3ccc(Cl)cc3)nc(Cl)nc21`
ZINC12502057	0.688	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC12502058	0.688	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC12933201	0.688	332.4 Da LogP 0.76 TPSA 115.8	✓ Ro5	✓ Clean	`Cn1ncc2c(NCc3ccc(CS(N)(=O)=O)cc3)ncnc21`
ZINC12941874	0.688	318.4 Da LogP 0.62 TPSA 115.8	✓ Ro5	✓ Clean	`Cn1ncc2c(NCc3ccc(S(N)(=O)=O)cc3)ncnc21`
ZINC13431057	0.688	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC25726736	0.688	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC3861746	0.688	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@@](=O)(O)…`
ZINC4354950	0.688	349.8 Da LogP 4.39 TPSA 55.6	✓ Ro5	✓ Clean	`Cc1ccc(-n2ncc3c(NCc4ccc(Cl)cc4)ncnc32)cc1`
ZINC52359382	0.688	311.4 Da LogP 2.90 TPSA 64.9	✓ Ro5	✓ Clean	`CC(C)OCc1ccc(CNc2ncnc3c2cnn3C)cc1`
ZINC82142138	0.688	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=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.