Protein profile

VK055_4511

ribonucleoside-diphosphate reductase, alpha subunit

Genome: KpATCC43816

Gene: AIK83049.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GWI4
Amino acids 701
Annotations 6
Features 32
PDB binders 14
Druggability 0.238

Overview

Basic information about this protein and its source genome.

Accession
VK055_4511
Gene
AIK83049.1
Status
annotated
Amino acids
701
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
32.99
Human E-value
5.47e-10
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
71.857
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
94.23

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 0.238
Structure A0A0H3GWI4
Pocket Pocket 45
P2Rank 0.777
Structure A0A0H3GWI4
Pocket Pocket 1
ColabFold model
FPocket 0.327 · Pocket 40
P2Rank 0.783 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 218 / 4744 genomes with a hit
Normalized 0.046

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:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • 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.
  • GO:0004748 Catalysis of the reaction: 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin. Thioredoxin disulfide is the oxidized form of thioredoxin.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
164 681 Pfam PF02867 Ribonucleotide reductase, barrel domain
164 681 InterPro IPR000788 Ribonucleotide reductase large subunit, C-terminal
2 701 NCBIfam TIGR04170 class 1b ribonucleoside-diphosphate reductase subunit alpha
2 701 InterPro IPR026459 Ribonucleotide reductase, class 1b, subunit NrdE
115 682 CDD cd01679 RNR_I
3 84 Pfam PF08343 Ribonucleotide reductase N-terminal
3 84 InterPro IPR013554 Ribonucleotide reductase N-terminal
162 685 SUPERFAMILY SSF51998 PFL-like glycyl radical enzymes
83 687 PANTHER PTHR11573 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE CHAIN
83 687 InterPro IPR039718 Ribonucleoside-diphosphate reductase large subunit
2 161 SUPERFAMILY SSF48168 R1 subunit of ribonucleotide reductase, N-terminal domain
2 161 InterPro IPR008926 Ribonucleotide reductase R1 subunit, N-terminal
147 682 Gene3D G3DSA:3.20.70.20 -
452 474 PRINTS PR01183 Ribonucleotide reductase large chain signature
452 474 InterPro IPR000788 Ribonucleotide reductase large subunit, C-terminal
238 257 PRINTS PR01183 Ribonucleotide reductase large chain signature
238 257 InterPro IPR000788 Ribonucleotide reductase large subunit, C-terminal
564 591 PRINTS PR01183 Ribonucleotide reductase large chain signature
564 591 InterPro IPR000788 Ribonucleotide reductase large subunit, C-terminal
413 436 PRINTS PR01183 Ribonucleotide reductase large chain signature
413 436 InterPro IPR000788 Ribonucleotide reductase large subunit, C-terminal
480 503 PRINTS PR01183 Ribonucleotide reductase large chain signature
480 503 InterPro IPR000788 Ribonucleotide reductase large subunit, C-terminal
369 380 PRINTS PR01183 Ribonucleotide reductase large chain signature
369 380 InterPro IPR000788 Ribonucleotide reductase large subunit, C-terminal
282 334 Gene3D G3DSA:1.10.1650.20 -
86 158 Pfam PF00317 Ribonucleotide reductase, all-alpha domain
86 158 InterPro IPR013509 Ribonucleotide reductase large subunit, N-terminal
553 575 ProSitePatterns PS00089 Ribonucleotide reductase large subunit signature.
553 575 InterPro IPR013346 Ribonucleotide reductase, class I, alpha subunit, C-terminal
90 683 NCBIfam TIGR02506 ribonucleoside-diphosphate reductase subunit alpha
90 683 InterPro IPR013346 Ribonucleotide reductase, class I, alpha subunit, C-terminal

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_A0A0H3GWI4
AlphaFold full sequence Viewing
ColabFold VK055_4511
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
45 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 10.11 0.544
2 3.53 0.13
3 3.21 0.11
4 2.86 0.09
5 1.62 0.026

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.

73 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…
7LL P23921 306.3 Da LogP 3.01 TPSA 81.9 ✓ Ro5 Alert c1ccc2c(c1)ccc(c2/C=N\NC(=O)c3ccccc3O)O
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 P50620 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.