Protein profile

KP13_07851

Ribonuclease PH

Genome: KpKP13

Gene: rph ANJ86562.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H4J2
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Amino acids 238
Annotations 7
Features 20
PDB binders 5
Druggability 0.499

Overview

Basic information about this protein and its source genome.

Accession
KP13_07851
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
rph ANJ86562.1
Status
annotated
Amino acids
238
Structure source
AlphaFold + ColabFold
EC
2.7.7.56
GO
GO:0000049 Binding to a transfer RNA. GO:0009022 Catalysis of the reaction: tRNA(n+1) + phosphate = tRNA(n) + a nucleoside diphosphate. GO:0008033 The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group. GO:0000175 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule. GO:0031125 Any process involved in forming the mature 3' end of an rRNA molecule. GO:0016075 The chemical reactions and pathways resulting in the breakdown of rRNA, ribosomal RNA, a structural constituent of ribosomes.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
38.028
Human E-value
6.71e-06
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
66.102
DEG E-value
3.58e-112
Localization
Cytoplasmic
ColabFold pLDDT
96.42

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 0.499
Structure A0A0H3H4J2
Pocket Pocket 2
P2Rank 0.565
Structure A0A0H3H4J2
Pocket Pocket 1
ColabFold model
FPocket 0.201 · Pocket 7
P2Rank 0.704 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 1570 / 4744 genomes with a hit
Normalized 0.331

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0000049 Binding to a transfer RNA.
  • GO:0009022 Catalysis of the reaction: tRNA(n+1) + phosphate = tRNA(n) + a nucleoside diphosphate.
  • GO:0008033 The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
  • GO:0000175 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
  • GO:0031125 Any process involved in forming the mature 3' end of an rRNA molecule.
  • GO:0016075 The chemical reactions and pathways resulting in the breakdown of rRNA, ribosomal RNA, a structural constituent of ribosomes.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
9 238 Gene3D G3DSA:3.30.230.70 -
9 238 InterPro IPR027408 PNPase/RNase PH domain superfamily
153 237 SUPERFAMILY SSF55666 Ribonuclease PH domain 2-like
153 237 InterPro IPR036345 Exoribonuclease, PH domain 2 superfamily
1 181 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like
1 181 InterPro IPR020568 Ribosomal protein S5 domain 2-type fold
2 233 PANTHER PTHR11953 EXOSOME COMPLEX COMPONENT
10 236 CDD cd11362 RNase_PH_bact
10 236 InterPro IPR002381 Ribonuclease PH, bacterial-type
157 222 Pfam PF03725 3' exoribonuclease family, domain 2
157 222 InterPro IPR015847 Exoribonuclease, phosphorolytic domain 2
2 236 NCBIfam TIGR01966 ribonuclease PH
2 236 InterPro IPR002381 Ribonuclease PH, bacterial-type
9 237 FunFam G3DSA:3.30.230.70:FF:000003 Ribonuclease PH
14 237 Hamap MF_00564 Ribonuclease PH [rph].
14 237 InterPro IPR002381 Ribonuclease PH, bacterial-type
10 140 Pfam PF01138 3' exoribonuclease family, domain 1
10 140 InterPro IPR001247 Exoribonuclease, phosphorolytic domain 1
116 128 ProSitePatterns PS01277 Ribonuclease PH signature.
116 128 InterPro IPR018336 Ribonuclease PH, 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.

3D visualization script Full viewer

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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_A0A0H3H4J2
AlphaFold — — full sequence — Viewing
ColabFold KP13_07851
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
2 0.499
15 0.064
1 0.004
6 0.0

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 12.41 0.565
2 1.26 0.011

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.

55 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
5GP
3GCM
A7ZS61 363.2 Da LogP -2.57 TPSA 206.0 1 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…
FLC
3GCM
A7ZS61 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
NHE
1R6L
P50597 207.3 Da LogP 0.80 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCS(=O)(=O)O
PPV
5XEX
Q2FZ20 178.0 Da LogP -0.81 TPSA 124.3 ✓ Ro5 ✓ Clean OP(=O)(O)OP(=O)(O)O
WO4
3H1C
P05055 247.8 Da LogP -2.62 TPSA 80.3 ✓ Ro5 ✓ Clean [O-][W](=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.