Protein profile

PA3807

nucleoside diphosphate kinase

Genome: NC_002516.2

Gene: PA3807 ndk Structure source: AlphaFold UniProt Q59636
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Amino acids 143
Annotations 11
Features 24
PDB binders 4
Druggability 0.509

Overview

Basic information about this protein and its source genome.

Accession
PA3807
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA3807 ndk
Status
annotated
Amino acids
143
Structure source
AlphaFold
EC
2.7.4.6
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0046872 Binding to a metal ion. GO:0004550 Catalysis of the reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate. GO:0042121 The chemical reactions and pathways resulting in the formation of alginic acid, a hydrophilic polysaccharide occurring in, for example, the cell walls of brown algae (brown seaweeds). GO:0006241 The chemical reactions and pathways resulting in the formation of CTP, cytidine 5'-triphosphate.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
51.389
Human E-value
7.4e-20
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Extracellular

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 0.509
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

10
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0046872 Binding to a metal ion.
  • GO:0004550 Catalysis of the reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
  • GO:0042121 The chemical reactions and pathways resulting in the formation of alginic acid, a hydrophilic polysaccharide occurring in, for example, the cell walls of brown algae (brown seaweeds).
  • GO:0006241 The chemical reactions and pathways resulting in the formation of CTP, cytidine 5'-triphosphate.
  • GO:0006183 The chemical reactions and pathways resulting in the formation of GTP, guanosine triphosphate.
  • GO:0006163 The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
  • GO:0006220 The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
  • GO:0006228 The chemical reactions and pathways resulting in the formation of UTP, uridine (5'-)triphosphate.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
1 140 SUPERFAMILY SSF54919 Nucleoside diphosphate kinase, NDK
1 140 InterPro IPR036850 Nucleoside diphosphate kinase-like domain superfamily
114 122 ProSitePatterns PS00469 Nucleoside diphosphate kinases active site.
114 122 InterPro IPR023005 Nucleoside diphosphate kinase, active site
1 140 Gene3D G3DSA:3.30.70.141 -
4 133 CDD cd04413 NDPk_I
3 138 Hamap MF_00451 Nucleoside diphosphate kinase [ndk].
3 138 InterPro IPR001564 Nucleoside diphosphate kinase
2 134 PANTHER PTHR46161 NUCLEOSIDE DIPHOSPHATE KINASE
3 140 SMART SM00562 ndk_5
3 140 InterPro IPR034907 Nucleoside diphosphate kinase-like domain
1 139 FunFam G3DSA:3.30.70.141:FF:000001 Nucleoside diphosphate kinase
4 137 Pfam PF00334 Nucleoside diphosphate kinase
4 137 InterPro IPR034907 Nucleoside diphosphate kinase-like domain
114 133 PRINTS PR01243 Nucleoside diphosphate kinase signature
114 133 InterPro IPR001564 Nucleoside diphosphate kinase
70 87 PRINTS PR01243 Nucleoside diphosphate kinase signature
70 87 InterPro IPR001564 Nucleoside diphosphate kinase
50 69 PRINTS PR01243 Nucleoside diphosphate kinase signature
50 69 InterPro IPR001564 Nucleoside diphosphate kinase
91 107 PRINTS PR01243 Nucleoside diphosphate kinase signature
91 107 InterPro IPR001564 Nucleoside diphosphate kinase
6 28 PRINTS PR01243 Nucleoside diphosphate kinase signature
6 28 InterPro IPR001564 Nucleoside diphosphate kinase

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
AlphaFold PA3807
AlphaFold — — 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 0.509

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.

54 records

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
DTT
3NGS
Q9U1E1 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
GNP
2DXF
O58429 522.2 Da LogP -2.76 TPSA 301.9 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
PHS
1WKL
Q5SLV5 82.0 Da LogP -0.64 TPSA 57.5 ✓ Ro5 ✓ Clean OP(=O)O
VO4
3Q8Y
Q5HFV4 114.9 Da LogP -3.69 TPSA 86.2 ✓ Ro5 ✓ Clean [O-][V](=O)([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.