Protein profile

PA1294

ribonuclease D

Genome: NC_002516.2

Gene: rnd PA1294 Structure source: AlphaFold UniProt Q9I450
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Amino acids 374
Annotations 11
Features 27
PDB binders 2
Druggability 0.35

Overview

Basic information about this protein and its source genome.

Accession
PA1294
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
rnd PA1294
Status
annotated
Amino acids
374
Structure source
AlphaFold
EC
3.1.13.5
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0000175 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule. GO:0003676 Binding to a nucleic acid. GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. GO:0033890 Catalysis of the exonucleolytic cleavage that removes extra residues from the 3'-terminus of tRNA to produce 5'-mononucleotides. GO:0042780 The process in which the 3' end of a pre-tRNA molecule is converted to that of a mature tRNA.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
27.719
Human E-value
7.24e-18
Gut microbiome off-target
hit
Essential (DEG)
N
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 0.35
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:0000175 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
  • GO:0003676 Binding to a nucleic acid.
  • GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
  • GO:0033890 Catalysis of the exonucleolytic cleavage that removes extra residues from the 3'-terminus of tRNA to produce 5'-mononucleotides.
  • GO:0042780 The process in which the 3' end of a pre-tRNA molecule is converted to that of a mature tRNA.
  • GO:0008033 The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
  • GO:0006139 Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
  • GO:0008408 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
  • GO:0044237 OBSOLETE. The chemical reactions and pathways by which individual cells transform chemical substances.

Sequence Features

Domain/signature hits from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
8 373 NCBIfam TIGR01388 ribonuclease D
8 373 InterPro IPR006292 Ribonuclease D
197 303 SUPERFAMILY SSF47819 HRDC-like
197 303 InterPro IPR010997 HRDC-like superfamily
212 292 ProSiteProfiles PS50967 HRDC domain profile.
212 292 InterPro IPR002121 HRDC domain
212 292 SMART SM00341 hrdc7
5 212 SUPERFAMILY SSF53098 Ribonuclease H-like
5 212 InterPro IPR012337 Ribonuclease H-like superfamily
6 173 Pfam PF01612 3'-5' exonuclease
6 173 InterPro IPR002562 3'-5' exonuclease domain
5 193 Gene3D G3DSA:3.30.420.10 -
5 193 InterPro IPR036397 Ribonuclease H superfamily
6 174 SMART SM00474 35exoneu6
6 174 InterPro IPR002562 3'-5' exonuclease domain
215 282 Pfam PF00570 HRDC domain
215 282 InterPro IPR002121 HRDC domain
2 373 PANTHER PTHR47649 RIBONUCLEASE D
6 372 Hamap MF_01899 Ribonuclease D [rnd].
6 372 InterPro IPR006292 Ribonuclease D
197 296 Gene3D G3DSA:1.10.150.80 HRDC domain
197 296 InterPro IPR044876 HRDC domain superfamily
303 374 Gene3D G3DSA:1.10.150.80 HRDC domain
303 374 InterPro IPR044876 HRDC domain superfamily
14 190 CDD cd06142 RNaseD_exo
297 372 SUPERFAMILY SSF47819 HRDC-like
297 372 InterPro IPR010997 HRDC-like superfamily

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 PA1294
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
2 0.35
10 0.325

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

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
A3P
7MPO
X5MEI1 427.2 Da LogP -1.75 TPSA 232.6 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
YT3
3SAF
Q01780 88.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Y+3]

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.