Protein profile

KP13_04750

Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase

Genome: KpKP13

Gene: AHE43713.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GVR2
Amino acids 355
Annotations 3
Features 24
PDB binders 26
Druggability 0.256

Overview

Basic information about this protein and its source genome.

Accession
KP13_04750
Gene
AHE43713.1
Status
annotated
Amino acids
355
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
96.54

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 0.256
Structure A0A0H3GVR2
Pocket Pocket 8
P2Rank 0.567
Structure A0A0H3GVR2
Pocket Pocket 1
ColabFold model
FPocket 0.251 · Pocket 12
P2Rank 0.478 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 60 / 4744 genomes with a hit
Normalized 0.013

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 2 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

2
  • GO:0008939 Catalysis of the reaction: 5,6-dimethylbenzimidazole + nicotinate D-ribonucleotide = alpha-ribazole 5'-phosphate + H+ + nicotinate.
  • GO:0009236 The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
4 346 PANTHER PTHR43463 NICOTINATE-NUCLEOTIDE--DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE
4 346 InterPro IPR003200 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase
1 2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
59 329 FunFam G3DSA:3.40.50.10210:FF:000001 Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
15 346 NCBIfam TIGR03160 nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
15 346 InterPro IPR017846 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, bacterial type
1 63 Gene3D G3DSA:1.10.1610.10 -
1 63 InterPro IPR023195 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, N-terminal
13 348 Hamap MF_00230 Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase [cobT].
13 348 InterPro IPR017846 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, bacterial type
324 353 Gene3D G3DSA:1.10.1610.10 -
324 353 InterPro IPR023195 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, N-terminal
5 345 SUPERFAMILY SSF52733 Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)
5 345 InterPro IPR036087 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase-like superfamily
64 323 Gene3D G3DSA:3.40.50.10210 -
64 323 InterPro IPR036087 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase-like superfamily
23 355 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
11 345 Pfam PF02277 Phosphoribosyltransferase
11 345 InterPro IPR003200 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase
12 22 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
31 343 CDD cd02439 DMB-PRT_CobT
31 343 InterPro IPR003200 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase
3 11 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 22 Phobius SIGNAL_PEPTIDE Signal peptide region

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_A0A0H3GVR2
AlphaFold full sequence Viewing
ColabFold KP13_04750
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
8 0.256
2 0.213

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 5.71 0.276
2 1.06 0.006

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.

76 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
13X F6MZ55 126.1 Da LogP 0.80 TPSA 60.7 ✓ Ro5 ✓ Clean c1c(cc(cc1O)O)O
150 Q05603 136.2 Da LogP 1.47 TPSA 52.0 ✓ Ro5 ✓ Clean Cc1cc(c(cc1C)N)N
1RB Q05603 330.2 Da LogP -0.24 TPSA 134.3 ✓ Ro5 ✓ Clean c1ccc2c(c1)ncn2[C@@H]3[C@@H]([C@@H]([C@H](O3)CO…
2AC Q05603 123.2 Da LogP 1.28 TPSA 46.2 ✓ Ro5 ✓ Clean Cc1ccc(c(c1)N)O
2AF Q05603 109.1 Da LogP 0.97 TPSA 46.2 ✓ Ro5 ✓ Clean c1ccc(c(c1)N)O
2MP Q05603 122.2 Da LogP 2.01 TPSA 20.2 ✓ Ro5 ✓ Clean Cc1ccc(cc1C)O
34A Q05603 121.2 Da LogP 1.89 TPSA 26.0 ✓ Ro5 ✓ Clean Cc1ccc(cc1C)N
5MB Q05603 132.2 Da LogP 1.87 TPSA 28.7 ✓ Ro5 ✓ Clean Cc1ccc2c(c1)[nH]cn2
5OB Q05603 148.2 Da LogP 1.57 TPSA 37.9 ✓ Ro5 ✓ Clean COc1ccc2c(c1)[nH]cn2
7RA Q05603 347.2 Da LogP -1.86 TPSA 186.1 ✓ Ro5 ✓ Clean c1c2c(ncn2[C@@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)…
7RP Q05603 332.2 Da LogP -1.45 TPSA 160.0 ✓ Ro5 ✓ Clean c1c2c(ncn1)ncn2[C@@H]3[C@@H]([C@@H]([C@H](O3)CO…
AAM Q05603 347.2 Da LogP -1.86 TPSA 186.1 ✓ Ro5 ✓ Clean c1nc(c2c(n1)ncn2[C@@H]3[C@@H]([C@@H]([C@H](O3)C…
ADE Q05603 135.1 Da LogP -0.06 TPSA 80.5 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)c(ncn2)N
BZI Q05603 118.1 Da LogP 1.56 TPSA 28.7 ✓ Ro5 ✓ Clean c1ccc2c(c1)[nH]cn2
DMD Q05603 146.2 Da LogP 2.18 TPSA 28.7 ✓ Ro5 ✓ Clean Cc1cc2c(cc1C)nc[nH]2
IND Q05603 117.2 Da LogP 2.17 TPSA 15.8 ✓ Ro5 ✓ Clean c1ccc2c(c1)cc[nH]2
IPH Q05603 94.1 Da LogP 1.39 TPSA 20.2 ✓ Ro5 ✓ Clean c1ccc(cc1)O
MCT Q05603 124.1 Da LogP 1.41 TPSA 40.5 ✓ Ro5 Alert Cc1ccc(c(c1)O)O
NCN Q05603 335.2 Da LogP -2.23 TPSA 160.5 ✓ Ro5 ✓ Clean c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P…
NIO Q05603 123.1 Da LogP 0.78 TPSA 50.2 ✓ Ro5 ✓ Clean c1cc(cnc1)C(=O)O
P2P Q05603 348.2 Da LogP -1.74 TPSA 180.3 ✓ Ro5 ✓ Clean c1c2c(ncn2[C@@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)…
PCR Q05603 108.1 Da LogP 1.70 TPSA 20.2 ✓ Ro5 ✓ Clean Cc1ccc(cc1)O
PMO Q05603 360.3 Da LogP -0.23 TPSA 143.5 ✓ Ro5 ✓ Clean COc1ccc2c(c1)ncn2[C@@H]3[C@@H]([C@@H]([C@H](O3)…
RBZ Q05603 358.3 Da LogP 0.38 TPSA 134.3 ✓ Ro5 ✓ Clean Cc1cc2c(cc1C)n(cn2)[C@@H]3[C@@H]([C@@H]([C@H](O…
RMB Q05603 344.3 Da LogP 0.07 TPSA 134.3 ✓ Ro5 ✓ Clean Cc1ccc2c(c1)ncn2[C@@H]3[C@@H]([C@@H]([C@H](O3)C…
XYD Q05603 121.2 Da LogP 1.89 TPSA 26.0 ✓ Ro5 ✓ Clean Cc1ccc(c(c1)N)C

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.