Protein profile

VK055_4510

ribonucleoside-diphosphate reductase subunit beta nrdF2

Genome: KpATCC43816

Gene: AIK83048.1 nrdF2 Structure source: AlphaFold + ColabFold UniProt A0A0H3GU80
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Amino acids 320
Annotations 6
Features 16
PDB binders 10
Druggability 0.548

Overview

Basic information about this protein and its source genome.

Accession
VK055_4510
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK83048.1 nrdF2
Status
annotated
Amino acids
320
Structure source
AlphaFold + ColabFold
EC
1.17.4.1
GO
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: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. GO:0046872 Binding to a metal ion. GO:0004748 Catalysis of the reaction: 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin. Thioredoxin disulfide is the oxidized form of thioredoxin.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
22.0
Human E-value
5.93e-07
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
71.924
DEG E-value
4.29e-174
Localization
Cytoplasmic
ColabFold pLDDT
91.67

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 0.548
Structure A0A0H3GU80
Pocket Pocket 1
P2Rank 0.115
Structure A0A0H3GU80
Pocket Pocket 1
ColabFold model
FPocket 0.68 · Pocket 11
P2Rank 0.188 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 292 / 4744 genomes with a hit
Normalized 0.062

Sequence

Primary amino-acid sequence viewer.

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: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.
  • GO:0046872 Binding to a metal ion.
  • GO:0004748 Catalysis of the reaction: 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin. Thioredoxin disulfide is the oxidized form of thioredoxin.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
10 281 CDD cd01049 RNRR2
10 281 InterPro IPR033909 Ribonucleotide reductase small subunit
1 317 PIRSF PIRSF000355 NrdB
1 317 InterPro IPR000358 Ribonucleotide reductase small subunit family
7 320 SUPERFAMILY SSF47240 Ferritin-like
7 320 InterPro IPR009078 Ferritin-like superfamily
9 309 PANTHER PTHR23409 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SMALL CHAIN
9 309 InterPro IPR000358 Ribonucleotide reductase small subunit family
10 281 Pfam PF00268 Ribonucleotide reductase, small chain
10 281 InterPro IPR000358 Ribonucleotide reductase small subunit family
1 292 Gene3D G3DSA:1.10.620.20 Ribonucleotide Reductase, subunit A
1 292 InterPro IPR012348 Ribonucleotide reductase-like
8 320 NCBIfam TIGR04171 class 1b ribonucleoside-diphosphate reductase subunit beta
8 320 InterPro IPR026494 Ribonucleoside-diphosphate reductase subunit beta
98 114 ProSitePatterns PS00368 Ribonucleotide reductase small subunit signature.
98 114 InterPro IPR030475 Ribonucleotide reductase small subunit, acitve 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_A0A0H3GU80
AlphaFold — — full sequence — Viewing
ColabFold VK055_4510
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
16 0.114
20 0.112
15 0.003

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 3.73 0.115
2 3.12 0.084
3 0.98 0.005
4 0.82 0.002

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.

60 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
AZI
1RSR
P69924 42.0 Da LogP 0.87 TPSA 58.7 ✓ Ro5 Alert [N-]=[N+]=[N-]
BTB
6QO8
Q81TB4 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
DAT
4ERM
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
5CNU
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
4ERM
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
2R2F
P17424 127.7 Da LogP -0.07 TPSA 9.2 ✓ Ro5 ✓ Clean O([Fe])[Fe]
O
1PIU
P69924 18.0 Da LogP -0.82 TPSA 31.5 ✓ Ro5 ✓ Clean O
OXY
1OQU
O69274 32.0 Da LogP 0.07 TPSA 34.1 ✓ Ro5 ✓ Clean O=O
PEO
3N3B
P37146 34.0 Da LogP 0.02 TPSA 40.5 ✓ Ro5 ✓ Clean OO
TTP
5CNV
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.