Protein profile

PA1156

ribonucleotide-diphosphate reductase subunit alpha

Genome: NC_002516.2

Gene: PA1156 nrdA Structure source: Experimental + AlphaFold UniProt Q9I4I1
Amino acids 963
Annotations 6
Features 37
PDB binders 18
Druggability 0.485

Overview

Basic information about this protein and its source genome.

Accession
PA1156
Gene
PA1156 nrdA
Status
annotated
Amino acids
963
Structure source
Experimental + AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
50.877
Human E-value
2.35e-30
Gut microbiome off-target
hit
Essential (DEG)
Y
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 0.485
Structure
Pocket

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:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • 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:0006260 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

37 records
Show feature table
Start End DB Term Name
750 771 ProSitePatterns PS00089 Ribonucleotide reductase large subunit signature.
750 771 InterPro IPR013346 Ribonucleotide reductase, class I, alpha subunit, C-terminal
294 365 Pfam PF00317 Ribonucleotide reductase, all-alpha domain
294 365 InterPro IPR013509 Ribonucleotide reductase large subunit, N-terminal
370 907 SUPERFAMILY SSF51998 PFL-like glycyl radical enzymes
1 25 MobiDBLite mobidb-lite consensus disorder prediction
371 906 Pfam PF02867 Ribonucleotide reductase, barrel domain
371 906 InterPro IPR000788 Ribonucleotide reductase large subunit, C-terminal
297 907 NCBIfam TIGR02506 ribonucleoside-diphosphate reductase subunit alpha
297 907 InterPro IPR013346 Ribonucleotide reductase, class I, alpha subunit, C-terminal
33 128 Pfam PF03477 ATP cone domain
33 128 InterPro IPR005144 ATP-cone domain
149 233 Pfam PF03477 ATP cone domain
149 233 InterPro IPR005144 ATP-cone domain
219 915 FunFam G3DSA:3.20.70.20:FF:000009 Ribonucleoside-diphosphate reductase
220 915 Gene3D G3DSA:3.20.70.20 -
32 132 ProSiteProfiles PS51161 ATP-cone domain profile.
32 132 InterPro IPR005144 ATP-cone domain
154 369 SUPERFAMILY SSF48168 R1 subunit of ribonucleotide reductase, N-terminal domain
154 369 InterPro IPR008926 Ribonucleotide reductase R1 subunit, N-terminal
148 237 ProSiteProfiles PS51161 ATP-cone domain profile.
148 237 InterPro IPR005144 ATP-cone domain
656 678 PRINTS PR01183 Ribonucleotide reductase large chain signature
656 678 InterPro IPR000788 Ribonucleotide reductase large subunit, C-terminal
684 707 PRINTS PR01183 Ribonucleotide reductase large chain signature
684 707 InterPro IPR000788 Ribonucleotide reductase large subunit, C-terminal
760 787 PRINTS PR01183 Ribonucleotide reductase large chain signature
760 787 InterPro IPR000788 Ribonucleotide reductase large subunit, C-terminal
446 465 PRINTS PR01183 Ribonucleotide reductase large chain signature
446 465 InterPro IPR000788 Ribonucleotide reductase large subunit, C-terminal
581 592 PRINTS PR01183 Ribonucleotide reductase large chain signature
581 592 InterPro IPR000788 Ribonucleotide reductase large subunit, C-terminal
618 641 PRINTS PR01183 Ribonucleotide reductase large chain signature
618 641 InterPro IPR000788 Ribonucleotide reductase large subunit, C-terminal
150 963 PANTHER PTHR11573 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE CHAIN
150 963 InterPro IPR039718 Ribonucleoside-diphosphate reductase large subunit
319 907 CDD cd01679 RNR_I

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

1 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 5IM3
X-ray 2.30 Å A,B
100.0% 1-963
Viewing
AlphaFold PA1156
AlphaFold 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
1 0.485
6 0.238

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 15.18 0.747
2 7.35 0.384
3 2.32 0.059
4 2.12 0.049
5 1.93 0.039

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.

77 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
DTP 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@]…

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.