Protein profile

PA1823

NADH pyrophosphatase

Genome: NC_002516.2

Gene: PA1823 nudC Structure source: AlphaFold UniProt O86062

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Amino acids 278

Annotations 12

Features 22

PDB binders 5

Druggability 0.823

Overview

Basic information about this protein and its source genome.

Accession: PA1823
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA1823 nudC
Status: annotated
Amino acids: 278
Structure source: AlphaFold

3.6.1.- 3.6.1.22

GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. GO:0000287 Binding to a magnesium (Mg) ion. GO:0030145 Binding to a manganese ion (Mn). GO:0000210 Catalysis of the reaction: NAD+ + H2O = AMP + NMN. GO:0035529 Catalysis of the reaction: NADH + H2O = AMP + NMNH + 2 H+. GO:0110153 Catalysis of the reaction: a 5'-end NAD+-phospho-ribonucleoside in mRNA + H2O = a 5'-end phospho-adenosine-phospho-ribonucleoside in mRNA + beta-nicotinamide D-ribonucleotide + 2 H+.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 50.0
Human E-value: 2.58e-24
Gut microbiome off-target: hit
Essential (DEG): N
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 0.823

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 10 GO

Enzyme Commission (EC)

Gene Ontology (GO)

GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
GO:0000287 Binding to a magnesium (Mg) ion.
GO:0030145 Binding to a manganese ion (Mn).
GO:0000210 Catalysis of the reaction: NAD+ + H2O = AMP + NMN.
GO:0035529 Catalysis of the reaction: NADH + H2O = AMP + NMNH + 2 H+.
GO:0110153 Catalysis of the reaction: a 5'-end NAD+-phospho-ribonucleoside in mRNA + H2O = a 5'-end phospho-adenosine-phospho-ribonucleoside in mRNA + beta-nicotinamide D-ribonucleotide + 2 H+.
GO:0008270 Binding to a zinc ion (Zn).
GO:0019677 The chemical reactions and pathways resulting in the breakdown of nicotinamide adenine dinucleotide (NAD+), a coenzyme that interconverts with its reduced form, NADH, in many redox and catabolic reactions.
GO:0006742 The chemical reactions and pathways resulting in the breakdown of nicotinamide adenine dinucleotide phosphate (NADP+), a coenzyme that interconverts with its reduced form, NADPH, in many redox and biosynthetic reactions.
GO:0046872 Binding to a metal ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records

Show feature table

Start	End	DB	Term	Name
145	258	Pfam	PF00293	NUDIX domain
145	258	InterPro	IPR000086	NUDIX hydrolase domain
94	260	SUPERFAMILY	SSF55811	Nudix
94	260	InterPro	IPR015797	NUDIX hydrolase-like domain superfamily
142	270	Gene3D	G3DSA:3.90.79.10	Nucleoside Triphosphate Pyrophosphohydrolase
5	141	FunFam	G3DSA:3.90.79.20:FF:000004	NADH pyrophosphatase
175	196	ProSitePatterns	PS00893	Nudix box signature.
175	196	InterPro	IPR020084	NUDIX hydrolase, conserved site
142	273	FunFam	G3DSA:3.90.79.10:FF:000004	NADH pyrophosphatase
5	141	Gene3D	G3DSA:3.90.79.20	-
141	265	ProSiteProfiles	PS51462	Nudix hydrolase domain profile.
141	265	InterPro	IPR000086	NUDIX hydrolase domain
19	107	Pfam	PF09296	NADH pyrophosphatase-like rudimentary NUDIX domain
19	107	InterPro	IPR015375	NADH pyrophosphatase-like, N-terminal
109	140	Pfam	PF09297	NADH pyrophosphatase zinc ribbon domain
109	140	InterPro	IPR015376	Zinc ribbon, NADH pyrophosphatase
8	112	SUPERFAMILY	SSF55811	Nudix
8	112	InterPro	IPR015797	NUDIX hydrolase-like domain superfamily
145	267	CDD	cd03429	NADH_pyrophosphatase
8	273	Hamap	MF_00297	NAD-capped RNA hydrolase NudC [nudC].
8	273	InterPro	IPR022925	NAD-capped RNA hydrolase NudC
79	266	PANTHER	PTHR42904	NUDIX HYDROLASE, NUDC SUBFAMILY

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

0 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA1823	AlphaFold	—	—	full sequence	—	Viewing

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				0.823

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.

55 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
2GE	5MZG	P53368	295.2 Da LogP 3.61 TPSA 63.8	✓ Ro5	✓ Clean	`c1cc(c(c(c1)Cl)Cl)c2cc(nc(n2)N)NC3CC3`
6OG	5OTN	Q7ZWC3	361.3 Da LogP -0.83 TPSA 175.1	✓ Ro5	✓ Clean	`COc1c2c(nc(n1)N)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO…`
8DG	5MZE	P53368	523.2 Da LogP -2.01 TPSA 298.8	3 viol.	✓ Clean	`C1[C@@H]([C@H](O[C@H]1N2C3=C(C(=O)NC(=N3)N)NC2=…`
MGP	6SCX	Q9BQG2	538.2 Da LogP -2.91 TPSA 290.1	3 viol.	✓ Clean	`C[n+]1cn(c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H](…`
NMN	5IW5	P32664	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(…`

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
ZINC12503278	1.000	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	1.000	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	1.000	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	1.000	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	1.000	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	1.000	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	1.000	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	1.000	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]…`
ZINC98208168	1.000	295.2 Da LogP 3.61 TPSA 63.8	✓ Ro5	✓ Clean	`Nc1nc(NC2CC2)cc(-c2cccc(Cl)c2Cl)n1`
ZINC4095572	0.809	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	0.809	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	0.809	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	0.809	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…`
ZINC25756940	0.760	331.3 Da LogP 0.35 TPSA 123.0	✓ Ro5	✓ Clean	`C[C@@H]1[C@@H](COP(=O)(O)O)O[C@@H]([n+]2cccc(C(…`
ZINC13099244	0.750	281.3 Da LogP -0.94 TPSA 128.5	✓ Ro5	✓ Clean	`COc1nc(N)nc2c1ncn2[C@@H]1C[C@@H](O)[C@@H](CO)O1`
ZINC1320041	0.750	281.3 Da LogP -0.94 TPSA 128.5	✓ Ro5	✓ Clean	`COc1nc(N)nc2c1ncn2[C@@H]1C[C@H](O)[C@@H](CO)O1`
ZINC4557107	0.750	281.3 Da LogP -0.94 TPSA 128.5	✓ Ro5	✓ Clean	`COc1nc(N)nc2c1ncn2[C@@H]1C[C@H](O)[C@H](CO)O1`
ZINC4557109	0.750	281.3 Da LogP -0.94 TPSA 128.5	✓ Ro5	✓ Clean	`COc1nc(N)nc2c1ncn2[C@H]1C[C@@H](O)[C@H](CO)O1`
ZINC1776011316	0.700	333.3 Da LogP -1.74 TPSA 154.2	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CCP(=O)(O)O)[C@@H…`
ZINC98208167	0.690	269.1 Da LogP 3.07 TPSA 63.8	✓ Ro5	✓ Clean	`CNc1cc(-c2cccc(Cl)c2Cl)nc(N)n1`
ZINC12371988	0.683	298.3 Da LogP -3.26 TPSA 150.5	✓ Ro5	✓ Clean	`C[n+]1cn([C@@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c2n…`
ZINC12371989	0.683	298.3 Da LogP -3.26 TPSA 150.5	✓ Ro5	✓ Clean	`C[n+]1cn([C@@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O)c2…`
ZINC14591885	0.683	298.3 Da LogP -3.26 TPSA 150.5	✓ Ro5	✓ Clean	`C[n+]1cn([C@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O)c2n…`
ZINC18130229	0.683	298.3 Da LogP -3.26 TPSA 150.5	✓ Ro5	✓ Clean	`C[n+]1cn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c2nc…`
ZINC19939880	0.683	298.3 Da LogP -3.26 TPSA 150.5	✓ Ro5	✓ Clean	`C[n+]1cn([C@@H]2O[C@H](CO)[C@H](O)[C@@H]2O)c2nc…`
ZINC28523740	0.683	298.3 Da LogP -3.26 TPSA 150.5	✓ Ro5	✓ Clean	`C[n+]1cn([C@@H]2O[C@H](CO)[C@H](O)[C@H]2O)c2nc(…`
ZINC5893253	0.683	298.3 Da LogP -3.26 TPSA 150.5	✓ Ro5	✓ Clean	`C[n+]1cn([C@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c2nc…`
ZINC104869865	0.682	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O…`
ZINC12504289	0.682	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC34541308	0.682	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC35000839	0.682	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC45284491	0.682	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC80639694	0.682	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC8215481	0.682	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC14613564	0.681	255.2 Da LogP -2.32 TPSA 116.9	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO)[C@@H](O)[C@@H…`
ZINC34633968	0.681	255.2 Da LogP -2.32 TPSA 116.9	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@H]2O[C@H](CO)[C@@H](O)[C@H]2…`
ZINC4096036	0.681	255.2 Da LogP -2.32 TPSA 116.9	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO)[C@@H](O)[C@H]…`
ZINC65748069	0.681	255.2 Da LogP -2.32 TPSA 116.9	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO)[C@H](O)[C@H]2…`
ZINC65748073	0.681	255.2 Da LogP -2.32 TPSA 116.9	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO)[C@H](O)[C@@H]…`
ZINC901659	0.681	255.2 Da LogP -2.32 TPSA 116.9	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@H]2O[C@@H](CO)[C@H](O)[C@@H]…`
ZINC14963209	0.623	295.3 Da LogP -0.55 TPSA 128.5	✓ Ro5	✓ Clean	`CCOc1nc(N)nc2c1ncn2[C@@H]1C[C@@H](O)[C@@H](CO)O1`
ZINC14963217	0.623	295.3 Da LogP -0.55 TPSA 128.5	✓ Ro5	✓ Clean	`CCOc1nc(N)nc2c1ncn2[C@@H]1C[C@H](O)[C@@H](CO)O1`
ZINC1763215	0.623	295.3 Da LogP -0.55 TPSA 128.5	✓ Ro5	✓ Clean	`CCOc1nc(N)nc2c1ncn2[C@@H]1C[C@H](O)[C@H](CO)O1`
ZINC5353141	0.623	295.3 Da LogP -0.55 TPSA 128.5	✓ Ro5	✓ Clean	`CCOc1nc(N)nc2c1ncn2[C@@H]1C[C@@H](O)[C@H](CO)O1`
ZINC100058967	0.594	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc(=O)c2ncn([C@H]3O[C@H](CO[P@](=O)(O)OP(=O)…`
ZINC12504287	0.594	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc(=O)c2ncn([C@@H]3O[C@@H](CO[P@@](=O)(O)OP(…`
ZINC12504288	0.594	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc(=O)c2ncn([C@H]3O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC31308647	0.594	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc(=O)c2ncn([C@@H]3O[C@@H](CO[P@@](=O)(O)OP(…`
ZINC1772707562	0.592	294.7 Da LogP 2.80 TPSA 84.1	✓ Ro5	✓ Clean	`Nc1nc(NC2CC2)cc(-c2cc(Cl)c(O)cc2F)n1`
ZINC77300688	0.585	325.3 Da LogP -1.19 TPSA 148.8	✓ Ro5	✓ Clean	`C[C@H](CO)Oc1nc(N)nc2c1ncn2[C@H]1C[C@H](O)[C@@H…`

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.