Protein profile

VK055_2460

nicotinate-nucleotide diphosphorylase

Genome: KpATCC43816

Gene: AIK81057.1 nadC Structure source: AlphaFold + ColabFold UniProt A0A0H3GJC5

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Amino acids 297

Annotations 6

Features 21

PDB binders 4

Druggability 0.283

Overview

Basic information about this protein and its source genome.

Accession: VK055_2460
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK81057.1 nadC
Status: annotated
Amino acids: 297
Structure source: AlphaFold + ColabFold

2.4.2.19

GO:0016763 Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor). 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:0004514 Catalysis of the reaction: CO2 + diphosphate + nicotinate D-ribonucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + 2 H+ + quinolinate. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0034213 The chemical reactions and pathways resulting in the breakdown of quinolinate, the anion of quinolinic acid, also known as 2,3-pyridinedicarboxylic acid.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 38.636
Human E-value: 1.05e-13
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 57.037
DEG E-value: 8.3e-101
Localization: Cytoplasmic
ColabFold pLDDT: 96.44

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 0.283

Structure A0A0H3GJC5

Pocket Pocket 3

P2Rank 0.583

Structure A0A0H3GJC5

Pocket Pocket 1

ColabFold model

FPocket 0.438 · Pocket 2

P2Rank 0.63 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 164 / 4744 genomes with a hit

Normalized 0.035

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)

2.4.2.19

Gene Ontology (GO)

GO:0016763 Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
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:0004514 Catalysis of the reaction: CO2 + diphosphate + nicotinate D-ribonucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + 2 H+ + quinolinate.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0034213 The chemical reactions and pathways resulting in the breakdown of quinolinate, the anion of quinolinic acid, also known as 2,3-pyridinedicarboxylic acid.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records

Show feature table

Start	End	DB	Term	Name
17	297	PIRSF	PIRSF006250	NadC_ModD
17	297	InterPro	IPR027277	Nicotinate-nucleotide pyrophosphorylase/Putative pyrophosphorylase ModD
139	291	Gene3D	G3DSA:3.20.20.70	Aldolase class I
139	291	InterPro	IPR013785	Aldolase-type TIM barrel
43	129	Pfam	PF02749	Quinolinate phosphoribosyl transferase, N-terminal domain
43	129	InterPro	IPR022412	Quinolinate phosphoribosyl transferase, N-terminal
27	296	NCBIfam	TIGR00078	carboxylating nicotinate-nucleotide diphosphorylase
27	296	InterPro	IPR004393	Nicotinate-nucleotide pyrophosphorylase
13	130	SUPERFAMILY	SSF54675	Nicotinate/Quinolinate PRTase N-terminal domain-like
131	295	Pfam	PF01729	Quinolinate phosphoribosyl transferase, C-terminal domain
131	295	InterPro	IPR002638	Quinolinate phosphoribosyl transferase, C-terminal
18	296	PANTHER	PTHR32179	NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE [CARBOXYLATING]
18	296	InterPro	IPR027277	Nicotinate-nucleotide pyrophosphorylase/Putative pyrophosphorylase ModD
131	296	SUPERFAMILY	SSF51690	Nicotinate/Quinolinate PRTase C-terminal domain-like
131	296	InterPro	IPR036068	Nicotinate phosphoribosyltransferase-like, C-terminal
24	295	CDD	cd01572	QPRTase
24	295	InterPro	IPR004393	Nicotinate-nucleotide pyrophosphorylase
34	294	Gene3D	G3DSA:3.90.1170.20	-
34	294	InterPro	IPR037128	Quinolinate phosphoribosyl transferase, N-terminal domain superfamily
145	286	FunFam	G3DSA:3.20.20.70:FF:000030	Nicotinate-nucleotide pyrophosphorylase, carboxylating
34	141	FunFam	G3DSA:3.90.1170.20:FF:000002	Nicotinate-nucleotide pyrophosphorylase [carboxylating]

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

Loading 3D structure...

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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_A0A0H3GJC5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_2460	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
3				0.283

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	Score	Probability
1	3.99	0.159
2	2.25	0.055
3	1.78	0.033
4	1.41	0.018
5	1.04	0.006

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
2				0.438

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	Score	Probability
1	4.2	0.171
2	3.68	0.139
3	2.62	0.076
4	1.31	0.014
5	0.93	0.004

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.

54 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.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
NCN	4I9A	I3LK75	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…`
NTM	2B7N	O25909	167.1 Da LogP 0.48 TPSA 87.5	✓ Ro5	✓ Clean	`c1cc(c(nc1)C(=O)O)C(=O)O`
PHT	2B7P	O25909	166.1 Da LogP 1.08 TPSA 74.6	✓ Ro5	✓ Clean	`c1ccc(c(c1)C(=O)O)C(=O)O`
SRT	2JBM	Q15274	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@H]([C@H](C(=O)O)O)(C(=O)O)O`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC4095572	0.830	336.2 Da LogP -1.60 TPSA 157.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@@H…`
ZINC77311659	0.830	336.2 Da LogP -1.60 TPSA 157.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@H]…`
ZINC77311660	0.830	336.2 Da LogP -1.60 TPSA 157.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@H]…`
ZINC77311661	0.830	336.2 Da LogP -1.60 TPSA 157.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@@H…`
ZINC105146	0.722	242.2 Da LogP 2.75 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1-c1ccccc1C(=O)O`
ZINC157193	0.700	226.2 Da LogP 2.62 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)c1ccccc1`
ZINC1604722	0.700	326.3 Da LogP 2.93 TPSA 108.7	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)CCC(=O)c1ccccc1C(=O)O`
ZINC12359024	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC13533920	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC1532740	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC1549593	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC2013424	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC3581021	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC3860635	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)C(=O)O`
ZINC5783661	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC6072527	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC135598	0.690	227.2 Da LogP 2.01 TPSA 67.3	✓ Ro5	✓ Clean	`O=C(c1ccccc1)c1cccnc1C(=O)O`
ZINC343335	0.690	227.2 Da LogP 2.01 TPSA 67.3	✓ Ro5	✓ Clean	`O=C(O)c1cccnc1C(=O)c1ccccc1`
ZINC12503278	0.673	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@@H…`
ZINC1532667	0.673	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@H]2O[C@@H](COP(=O)(O)O)[C@H]…`
ZINC2545161	0.673	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@@H](COP(=O)(O)O)[C@H…`
ZINC3870109	0.673	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@@H](COP(=O)(O)O)[C@@…`
ZINC40465856	0.673	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@H]…`
ZINC40762833	0.673	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@H]2O[C@H](COP(=O)(O)O)[C@@H]…`
ZINC4228273	0.673	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@@H…`
ZINC77311638	0.673	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@H]…`
ZINC1600331	0.667	330.2 Da LogP 2.15 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)O)c1-c1c(C(=O)O)cccc1C(=O)O`
ZINC1296728	0.654	244.2 Da LogP 1.54 TPSA 100.4	✓ Ro5	✓ Clean	`O=C(O)c1ncccc1-c1cccnc1C(=O)O`
ZINC47217	0.654	244.2 Da LogP 1.54 TPSA 100.4	✓ Ro5	✓ Clean	`O=C(O)c1cccnc1-c1ncccc1C(=O)O`
ZINC164706	0.650	201.0 Da LogP 2.15 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1Br`
ZINC90931	0.650	248.0 Da LogP 1.99 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1I`
ZINC4096931	0.646	256.2 Da LogP -1.72 TPSA 111.1	✓ Ro5	✓ Clean	`O=C(O)c1ccc[n+]([C@@H]2O[C@H](CO)[C@@H](O)[C@H]…`
ZINC343704	0.636	208.2 Da LogP 1.04 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CC(=O)c1ccccc1C(=O)O`
ZINC39055766	0.636	218.1 Da LogP 2.13 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)C(F)(F)F`
ZINC394370	0.636	270.2 Da LogP 2.31 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccccc2C(=O)O)cc1`
ZINC4394109	0.636	382.4 Da LogP 1.68 TPSA 115.2	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)N1CCN(C(=O)c2ccccc2C(=O)O)CC1`
ZINC388710	0.632	210.1 Da LogP 0.78 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)O)c1C(=O)O`
ZINC389564	0.632	216.2 Da LogP 2.24 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)O)c2ccccc12`
ZINC45070868	0.632	216.2 Da LogP 2.24 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1cccc2c(C(=O)O)cccc12`
ZINC391925	0.625	254.1 Da LogP 0.48 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(=O)O)c(C(=O)O)cc1C(=O)O`
ZINC154566	0.619	257.2 Da LogP 2.83 TPSA 86.6	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1Nc1ccccc1C(=O)O`
ZINC256346309	0.619	270.2 Da LogP 3.50 TPSA 99.3	✓ Ro5	Alert	`O=C(O)c1ccccc1N=Nc1ccccc1C(=O)O`
ZINC3845505	0.619	268.3 Da LogP 3.25 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1/C=C/c1ccccc1C(=O)O`
ZINC410108	0.619	258.2 Da LogP 2.88 TPSA 83.8	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1Oc1ccccc1C(=O)O`
ZINC5369059	0.619	274.3 Da LogP 3.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1Sc1ccccc1C(=O)O`
ZINC5771961	0.619	256.3 Da LogP 2.67 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1Cc1ccccc1C(=O)O`
ZINC62723773	0.619	270.2 Da LogP 3.50 TPSA 99.3	✓ Ro5	Alert	`O=C(O)c1ccccc1/N=N/c1ccccc1C(=O)O`
ZINC3843351	0.609	358.3 Da LogP 2.10 TPSA 127.2	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)OCCOC(=O)c1ccccc1C(=O)O`
ZINC4178076	0.609	404.4 Da LogP 3.59 TPSA 132.8	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)Nc1ccccc1NC(=O)c1ccccc1C(=O)O`
ZINC518924	0.609	284.3 Da LogP 2.51 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1CC(=O)c1ccccc1C(=O)O`

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.