Protein profile

PA4669

4-diphosphocytidyl-2C-methyl-D-erythritol kinase

Genome: NC_002516.2

Gene: ipk Structure source: ColabFold

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Amino acids 282

Annotations 3

Features 20

PDB binders 2

Druggability 0.693

Overview

Basic information about this protein and its source genome.

Accession: PA4669
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: ipk
Status: annotated
Amino acids: 282
Structure source: ColabFold

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. 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:0050515 Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP + 2 H+.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Unknown

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 0.693

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MSVRLSLPAPAKLNLFLHILGRRDDGYHELQTLFQFLDHGDELHFEARQDGQVRLHTEIAGVPHDSNLIVRAARGLQEASGSPQGVDIWLDKRLPMGGGIGGGSSDAATTLLALNHLWQLGWDEDRIAALGLRLGADVPVFTRGRAAFAEGVGEKLTPVDIPEPWYLVVVPQVLVSTAEIFSDPLLTRDSPAIKVRTVLEGDSRNDCQPVVERRYPEVRNALILLNKFVSARLTGTGGCVFGSFPNKAEADKVSALLPDHLQRFVAKGSNISMLHRKLETLV

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
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:0050515 Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP + 2 H+.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records

Show feature table

Start	End	DB	Term	Name
3	262	PANTHER	PTHR43527	4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE, CHLOROPLASTIC
4	278	NCBIfam	TIGR00154	4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase
4	278	InterPro	IPR004424	4-diphosphocytidyl-2C-methyl-D-erythritol kinase
7	158	SUPERFAMILY	SSF54211	Ribosomal protein S5 domain 2-like
7	158	InterPro	IPR020568	Ribosomal protein S5 domain 2-type fold
1	160	FunFam	G3DSA:3.30.230.10:FF:000022	4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
160	277	SUPERFAMILY	SSF55060	GHMP Kinase, C-terminal domain
160	277	InterPro	IPR036554	GHMP kinase, C-terminal domain superfamily
3	279	PIRSF	PIRSF010376	IspE
3	279	InterPro	IPR004424	4-diphosphocytidyl-2C-methyl-D-erythritol kinase
5	271	Hamap	MF_00061	Putative 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase [ispE].
5	271	InterPro	IPR004424	4-diphosphocytidyl-2C-methyl-D-erythritol kinase
1	160	Gene3D	G3DSA:3.30.230.10	-
1	160	InterPro	IPR014721	Ribosomal protein S5 domain 2-type fold, subgroup
162	279	Gene3D	G3DSA:3.30.70.890	-
162	279	InterPro	IPR036554	GHMP kinase, C-terminal domain superfamily
87	144	Pfam	PF00288	GHMP kinases N terminal domain
87	144	InterPro	IPR006204	GHMP kinase N-terminal domain
205	254	Pfam	PF08544	GHMP kinases C terminal
205	254	InterPro	IPR013750	GHMP kinase, C-terminal domain

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 + 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 PA4669	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
1				0.693
2				0.319

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.

52 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
ANP	3PYF	P9WKG7	506.2 Da LogP -2.06 TPSA 281.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
CDM	3PYE	P9WKG7	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@…`

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).

No ChEMBL hits found through similar proteins.

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
ZINC12360002	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12360703	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12503599	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC16546165	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@](=O)(O)OP(=O)(…`
ZINC31977053	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC4806433	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC53683898	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC8586020	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC8586022	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
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…`
ZINC13518964	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC1571045	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC2046931	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O…`
ZINC4806442	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8613167	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC4096224	0.729	346.2 Da LogP -1.90 TPSA 191.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](N)(=O)O)[C@@…`
ZINC12503850	0.726	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141161066	0.726	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141163786	0.726	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC4228246	0.726	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OS(=O…`
ZINC105372833	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC105372837	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC17107643	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC204538551	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC31475423	0.703	434.3 Da LogP -2.99 TPSA 238.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@@](=O)(O)OC(=O)…`
ZINC105469665	0.694	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)CP(=O…`
ZINC13527614	0.694	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)CP(=O)…`
ZINC219330894	0.694	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)CP(=O)…`
ZINC3873852	0.694	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)CP(=O)…`
ZINC3873853	0.694	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@](=O)(O)CP(=O…`
ZINC3873854	0.694	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)CP(=O)…`
ZINC3873855	0.694	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@](=O)(O)CP(=O…`
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…`
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…`
ZINC13431059	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)(…`
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)…`
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.