Protein profile

VK055_1861

nicotinate (nicotinamide) nucleotide adenylyltransferase

Genome: KpATCC43816

Gene: nadD AIK80467.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GLD7
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Amino acids 213
Annotations 7
Features 16
PDB binders 7
Druggability 0.492

Overview

Basic information about this protein and its source genome.

Accession
VK055_1861
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
nadD AIK80467.1
Status
annotated
Amino acids
213
Structure source
AlphaFold + ColabFold
EC
2.7.7.18
GO
GO:0016779 Catalysis of the transfer of a nucleotidyl group from one compound (donor) to another (acceptor). GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0009435 The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD+), a coenzyme that interconverts with its reduced form, NADH, in many redox and catabolic reactions. NAD+ is derived from various sources including vitamin B3. GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0004515 Catalysis of the reaction: nicotinate beta-D-ribonucleotide + ATP + H+ = deamido-NAD+ + diphosphate.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
26.695
Human E-value
8.97e-07
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
76.415
DEG E-value
4.54e-122
Localization
Cytoplasmic
ColabFold pLDDT
94.3

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 0.492
Structure A0A0H3GLD7
Pocket Pocket 8
P2Rank 0.968
Structure A0A0H3GLD7
Pocket Pocket 1
ColabFold model
FPocket 0.152 · Pocket 2
P2Rank 0.948 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 112 / 4744 genomes with a hit
Normalized 0.024

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:0016779 Catalysis of the transfer of a nucleotidyl group from one compound (donor) to another (acceptor).
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0009435 The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD+), a coenzyme that interconverts with its reduced form, NADH, in many redox and catabolic reactions. NAD+ is derived from various sources including vitamin B3.
  • GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0004515 Catalysis of the reaction: nicotinate beta-D-ribonucleotide + ATP + H+ = deamido-NAD+ + diphosphate.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
2 212 Gene3D G3DSA:3.40.50.620 HUPs
2 212 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
7 187 Pfam PF01467 Cytidylyltransferase-like
7 187 InterPro IPR004821 Cytidyltransferase-like domain
6 68 NCBIfam TIGR00125 cytidyltransferase-like domain
6 68 InterPro IPR004821 Cytidyltransferase-like domain
3 213 Hamap MF_00244 Probable nicotinate-nucleotide adenylyltransferase [nadD].
3 213 InterPro IPR005248 Nicotinate/nicotinamide nucleotide adenylyltransferase
2 213 FunFam G3DSA:3.40.50.620:FF:000039 Probable nicotinate-nucleotide adenylyltransferase
4 212 SUPERFAMILY SSF52374 Nucleotidylyl transferase
7 212 NCBIfam TIGR00482 nicotinate (nicotinamide) nucleotide adenylyltransferase
7 212 InterPro IPR005248 Nicotinate/nicotinamide nucleotide adenylyltransferase
4 212 PANTHER PTHR39321 NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE-RELATED
4 212 InterPro IPR005248 Nicotinate/nicotinamide nucleotide adenylyltransferase
6 212 CDD cd02165 NMNAT
6 212 InterPro IPR005248 Nicotinate/nicotinamide nucleotide adenylyltransferase

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_A0A0H3GLD7
AlphaFold — — full sequence — Viewing
ColabFold VK055_1861
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
1 0.101
2 0.001
6 0.0
12 0.0

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 50.15 0.968

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.

57 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
DND
1KAQ
P54455 665.4 Da LogP -2.42 TPSA 312.5 3 viol. ✓ Clean c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(…
E9A
6BUV
P9WJJ5 435.6 Da LogP 5.05 TPSA 44.3 1 viol. ✓ Clean C[C@H]1CC[C@@H]([C@@H](C1)OC(=O)C[n+]2c3ccccc3n…
JJZ
3MLA
C3L5T6 429.9 Da LogP 5.52 TPSA 70.6 1 viol. ✓ Clean c1ccc2c(c1)cc3ccccc3c2C=NNC(=O)CCC(=O)Nc4cccc(c…
KJZ
3MMX
C3L5T6 437.9 Da LogP 4.16 TPSA 99.1 ✓ Ro5 ✓ Clean c1ccc2c(c1)cccc2/C=N/N(CC(=O)O)C(=O)CCC(=O)Nc3c…
LJZ
3MLB
C3L5T6 579.4 Da LogP 5.26 TPSA 141.8 2 viol. Alert c1cc(c(cc1)Cl)NC(=O)CCC(=O)/N=N/C=C2C=CC(=C/N=N…
NCN
1YUM
Q9HX21 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…
XE
1K4K
P0A752 131.3 Da LogP 0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Xe]

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.