Protein target profile

PA1155

ribonucleotide-diphosphate reductase subunit beta

Genome: NC_002516.2

Gene: PA1155 nrdB 3D evidence: AlphaFold DB model UniProt Q9I4I2
Length 415
Pocket druggability 0.715
Ligand records 62
EC / GO 1 / 5
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

4 signals
How to read this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal TPW pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Overview

Basic information about this protein and its source genome.

Accession
PA1155
Gene
PA1155 nrdB
Status
annotated
Amino acids
415
3D evidence
AlphaFold DB model

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
28.824
Human E-value
8.17e-40
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected pocket evidence

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.715
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MLSWDEFDKEDPTEAKAAPAAAQAVAQGHDKLDDEAAGSVEEARAVSADDSDAVARAKKALNDLDIQEGLDDLEGSAARVQVGDKQMINARADLNQLVPFKYDWAWQKYLDGCANHWMPQEVNMNADIALWKSKDGLSEDERRIVMRNLGFFSTADSLVANNLVLAVYRLITNPECRQYILRQAFEEAIHTHAYQYCIESLGMDEGEIFNMYHEIPSVAKKASWGLKYTRSISDPMFQTGTPETDRQFLRNLIAYYCVLEGIFFYCGFTQILSMGRRNKMTGTAEQFQYILRDESMHLNFGIDVINQIKIENPHLWDAQMKDEATQMILQGTQLEIEYARDTMPRGVLGMNAAMMEDYLKFIANRRLTQIGLKEEYPGTTNPFPWMSEIMDLKKEKNFFETRVIEYQTGGALSWD

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0005971 An enzyme complex composed of 2-4 or more subunits, which usually contains nonheme iron and requires ATP for catalysis. Catalyzes the formation of 2'-deoxyribonucleoside diphosphate from ribonucleoside diphosphate, using either thioredoxin disulfide or glutaredoxin disulfide as an acceptor.
  • GO:0005506 Binding to an iron (Fe) ion.
  • GO:0004748 Catalysis of the reaction: 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin. Thioredoxin disulfide is the oxidized form of thioredoxin.
  • GO:0009263 The chemical reactions and pathways resulting in the formation of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
1 252 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
56 388 SUPERFAMILY SSF47240 Ferritin-like
56 388 InterPro IPR009078 Ferritin-like superfamily
273 415 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
252 274 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
68 396 Gene3D G3DSA:1.10.620.20 Ribonucleotide Reductase, subunit A
68 396 InterPro IPR012348 Ribonucleotide reductase-like
253 272 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 48 MobiDBLite mobidb-lite consensus disorder prediction
64 415 PIRSF PIRSF000355 NrdB
64 415 InterPro IPR000358 Ribonucleotide reductase small subunit family
28 48 MobiDBLite mobidb-lite consensus disorder prediction
95 391 CDD cd01049 RNRR2
95 391 InterPro IPR033909 Ribonucleotide reductase small subunit
92 410 PANTHER PTHR23409 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SMALL CHAIN
92 410 InterPro IPR000358 Ribonucleotide reductase small subunit family
68 396 FunFam G3DSA:1.10.620.20:FF:000003 Ribonucleoside-diphosphate reductase subunit beta
1 15 MobiDBLite mobidb-lite consensus disorder prediction
95 382 Pfam PF00268 Ribonucleotide reductase, small chain
95 382 InterPro IPR000358 Ribonucleotide reductase small subunit family

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

3D visualization script Full viewer

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Structural evidence

0 + 1

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB PA1155
AlphaFold DB full sequence Viewing
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #1
0.677
Show in viewer

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.

62 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 62 via homologs
Structural ligands 8 0 loaded crystals
Bioactive compounds 4 50 ZINC proposed compounds
Drug-like & clean 36 1 PAINS alerts
Best available ligand signal
AZI PDB via homolog 42.0 Da · LogP 0.87 · TPSA 58.7 Open detail RCSB PDB
Detail RCSB PDB AZI PDB via homolog
Detail RCSB PDB BTB PDB via homolog
Detail RCSB PDB DAT PDB via homolog
Detail RCSB PDB DGT PDB via homolog

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
AZI RCSB PDB P69924 42.0 Da LogP 0.87 TPSA 58.7 ✓ Ro5 Alert [N-]=[N+]=[N-]
BTB RCSB PDB Q81TB4 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
DAT RCSB PDB P69924 411.2 Da LogP -0.72 TPSA 212.4 1 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@]…
DGT RCSB PDB P69924 507.2 Da LogP -1.31 TPSA 278.9 3 viol. ✓ Clean c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(O)O…
DTP RCSB PDB P69924 491.2 Da LogP -0.60 TPSA 258.9 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@]…
FEO RCSB PDB P69924 127.7 Da LogP -0.07 TPSA 9.2 ✓ Ro5 ✓ Clean O([Fe])[Fe]
O RCSB PDB P69924 18.0 Da LogP -0.82 TPSA 31.5 ✓ Ro5 ✓ Clean O
TTP RCSB PDB P69924 482.2 Da LogP -1.16 TPSA 244.1 2 viol. ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…

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.