Protein profile

PA5497

ribonucleoside-diphosphate reductase

Genome: NC_002516.2

Gene: PA5497 nrdJa Structure source: AlphaFold UniProt Q9HT76
Amino acids 734
Annotations 7
Features 22
PDB binders 16
Druggability 0.588

Overview

Basic information about this protein and its source genome.

Accession
PA5497
Gene
PA5497 nrdJa
Status
annotated
Amino acids
734
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
24.486
Human E-value
7.08e-31
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 0.588
Structure
Pocket

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:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0031419 Binding to cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
  • 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:0071897 The biosynthetic process resulting in the formation of DNA.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
95 671 CDD cd02888 RNR_II_dimer
95 671 InterPro IPR013344 Ribonucleotide reductase, adenosylcobalamin-dependent
412 434 PRINTS PR01183 Ribonucleotide reductase large chain signature
412 434 InterPro IPR000788 Ribonucleotide reductase large subunit, C-terminal
197 216 PRINTS PR01183 Ribonucleotide reductase large chain signature
197 216 InterPro IPR000788 Ribonucleotide reductase large subunit, C-terminal
374 397 PRINTS PR01183 Ribonucleotide reductase large chain signature
374 397 InterPro IPR000788 Ribonucleotide reductase large subunit, C-terminal
336 347 PRINTS PR01183 Ribonucleotide reductase large chain signature
336 347 InterPro IPR000788 Ribonucleotide reductase large subunit, C-terminal
440 463 PRINTS PR01183 Ribonucleotide reductase large chain signature
440 463 InterPro IPR000788 Ribonucleotide reductase large subunit, C-terminal
528 555 PRINTS PR01183 Ribonucleotide reductase large chain signature
528 555 InterPro IPR000788 Ribonucleotide reductase large subunit, C-terminal
14 672 FunFam G3DSA:3.20.70.20:FF:000040 Vitamin B12-dependent ribonucleotide reductase
43 678 NCBIfam TIGR02504 adenosylcobalamin-dependent ribonucleoside-diphosphate reductase
43 678 InterPro IPR013344 Ribonucleotide reductase, adenosylcobalamin-dependent
123 669 Pfam PF02867 Ribonucleotide reductase, barrel domain
123 669 InterPro IPR000788 Ribonucleotide reductase large subunit, C-terminal
15 725 PANTHER PTHR43371 VITAMIN B12-DEPENDENT RIBONUCLEOTIDE REDUCTASE
14 672 Gene3D G3DSA:3.20.70.20 -
35 710 SUPERFAMILY SSF51998 PFL-like glycyl radical enzymes

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 + 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 PA5497
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
21 0.413
5 0.307
4 0.201

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.

75 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
2A5 P21524 455.3 Da LogP -1.11 TPSA 232.6 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
3X4 P23921 418.5 Da LogP -0.12 TPSA 158.9 ✓ Ro5 ✓ Clean CC(C)(C(=O)NCCCC[C@H](C(=O)O)N)NC(=O)CN1C(=O)c2…
5AD O33839 251.2 Da LogP -0.95 TPSA 119.3 ✓ Ro5 ✓ Clean C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
7LL P23921 306.3 Da LogP 3.01 TPSA 81.9 ✓ Ro5 Alert c1ccc2c(c1)ccc(c2/C=N\NC(=O)c3ccccc3O)O
ADN O33839 267.2 Da LogP -1.98 TPSA 139.5 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ANP P21524 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
DCP Q08698 467.2 Da LogP -1.18 TPSA 250.2 2 viol. ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@@](=…
DGT Q08698 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 Q08698 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@]…
E4X P23921 488.4 Da LogP 4.10 TPSA 105.1 ✓ Ro5 ✓ Clean C[C@H](c1cccc2c1cccc2)[C@@H](C3=NNC(=O)O3)NS(=O…
E6O P23921 476.9 Da LogP 2.43 TPSA 148.2 ✓ Ro5 ✓ Clean C[C@H](c1cccc2c1CCC2)[C@@H](C3=NNC(=O)O3)NS(=O)…
EJ6 P23921 511.0 Da LogP 3.42 TPSA 117.5 1 viol. ✓ Clean Cc1ccc(c(c1C)[C@@H](C)[C@@H](C2=NNC(=O)O2)NS(=O…
GCQ P21524 423.2 Da LogP -1.05 TPSA 203.7 ✓ Ro5 ✓ Clean C1=CN(C(=O)N=C1N)[C@H]2C([C@@H]([C@H](O2)CO[P@]…
MRT P21524 1031.2 Da LogP 4.98 TPSA 286.9 3 viol. ✓ Clean CC(C)C[C@@H](C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](…
N5P P21524 518.2 Da LogP 1.54 TPSA 237.3 2 viol. ✓ Clean c1cc2c(ccn2C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(…
TTP P23921 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.