Protein profile

KP13_01374

NADH pyrophosphatase

Genome: KpKP13

Gene: nudC AHE46925.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GHB2

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Amino acids 257

Annotations 13

Features 20

PDB binders 7

Druggability 0.07

Overview

Basic information about this protein and its source genome.

Accession: KP13_01374
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: nudC AHE46925.1
Status: annotated
Amino acids: 257
Structure source: AlphaFold + ColabFold

3.6.1.- 3.6.1.22

GO:0000210 Catalysis of the reaction: NAD+ + H2O = AMP + NMN. GO:0046872 Binding to a metal ion. GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0000287 Binding to a magnesium (Mg) ion. GO:0030145 Binding to a manganese ion (Mn).

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 40.741
Human E-value: 1.43e-19
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 96.6

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 0.07

Structure A0A0H3GHB2

Pocket Pocket 9

P2Rank 0.872

Structure A0A0H3GHB2

Pocket Pocket 1

ColabFold model

FPocket 0.083 · Pocket 15

P2Rank 0.824 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 116 / 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.

2 EC 11 GO

Enzyme Commission (EC)

Gene Ontology (GO)

GO:0000210 Catalysis of the reaction: NAD+ + H2O = AMP + NMN.
GO:0046872 Binding to a metal ion.
GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0000287 Binding to a magnesium (Mg) ion.
GO:0030145 Binding to a manganese ion (Mn).
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.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records

Show feature table

Start	End	DB	Term	Name
1	125	Gene3D	G3DSA:3.90.79.20	-
3	96	SUPERFAMILY	SSF55811	Nudix
3	96	InterPro	IPR015797	NUDIX hydrolase-like domain superfamily
62	252	PANTHER	PTHR42904	NUDIX HYDROLASE, NUDC SUBFAMILY
126	257	Gene3D	G3DSA:3.90.79.10	Nucleoside Triphosphate Pyrophosphohydrolase
132	234	Pfam	PF00293	NUDIX domain
132	234	InterPro	IPR000086	NUDIX hydrolase domain
129	250	CDD	cd03429	NADH_pyrophosphatase
1	257	Hamap	MF_00297	NAD-capped RNA hydrolase NudC [nudC].
1	257	InterPro	IPR022925	NAD-capped RNA hydrolase NudC
125	248	ProSiteProfiles	PS51462	Nudix hydrolase domain profile.
125	248	InterPro	IPR000086	NUDIX hydrolase domain
1	125	FunFam	G3DSA:3.90.79.20:FF:000001	NADH pyrophosphatase
159	180	ProSitePatterns	PS00893	Nudix box signature.
159	180	InterPro	IPR020084	NUDIX hydrolase, conserved site
79	241	SUPERFAMILY	SSF55811	Nudix
79	241	InterPro	IPR015797	NUDIX hydrolase-like domain superfamily
93	124	Pfam	PF09297	NADH pyrophosphatase zinc ribbon domain
93	124	InterPro	IPR015376	Zinc ribbon, NADH pyrophosphatase
126	257	FunFam	G3DSA:3.90.79.10:FF:000004	NADH pyrophosphatase

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_A0A0H3GHB2	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01374	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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				18.98	0.833
2				0.8	0.003

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				15.55	0.756

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

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
2ME	5WWD	Q9CA40	60.1 Da LogP 0.65 TPSA 9.2	✓ Ro5	✓ Clean	`CCOC`
8DG	6FL4	Q9CA40	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=…`
GPP	5GP0	Q9CA40	314.2 Da LogP 2.91 TPSA 113.3	✓ Ro5	✓ Clean	`CC(=CCC/C(=C/CO[P@@](=O)(O)OP(=O)(O)O)/C)C`
IPR	6DBZ	Q9CA40	248.1 Da LogP 1.26 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)CCO[P@@](=O)(O)OP(=O)(O)O`
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](…`
NH4	5WWD	Q9CA40	18.0 Da LogP 0.38 TPSA 36.5	✓ Ro5	✓ Clean	`[NH4+]`
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…`
ZINC2579357	1.000	248.1 Da LogP 1.26 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)CCO[P@](=O)(O)OP(=O)(O)O`
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]…`
ZINC8215849	1.000	314.2 Da LogP 2.91 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CO[P@@](=O)(O)OP(=O)(O)O`
ZINC12494625	0.969	382.3 Da LogP 4.63 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CC/C(C)=C/CO[P@@](=O)(O)OP(=O)…`
ZINC2356589248	0.969	382.3 Da LogP 4.63 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCCC(C)=CCCC(C)=CCO[P@](=O)(O)OP(=O)(O)O`
ZINC34661063	0.939	394.2 Da LogP 3.02 TPSA 159.8	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CO[P@@](=O)(O)O[P@@](=O)(O)OP(…`
ZINC8218174	0.912	462.3 Da LogP 4.75 TPSA 159.8	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CC/C(C)=C/CO[P@@](=O)(O)O[P@@]…`
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(…`
ZINC1532829	0.758	234.2 Da LogP 2.79 TPSA 66.8	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/COP(=O)(O)O`
ZINC2556391	0.735	302.4 Da LogP 4.51 TPSA 66.8	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O)O`
ZINC8215740	0.719	246.1 Da LogP 1.18 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCO[P@@](=O)(O)OP(=O)(O)O`
ZINC12503703	0.708	427.2 Da LogP -1.42 TPSA 232.3	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@@H](CO[P@@](=O)(…`
ZINC8215878	0.708	427.2 Da LogP -1.42 TPSA 232.3	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O…`
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…`
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]…`
ZINC71769106	0.676	326.1 Da LogP 1.30 TPSA 159.8	✓ Ro5	✓ Clean	`CC(C)=CCO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O`
ZINC12502182	0.667	283.2 Da LogP -2.36 TPSA 159.2	✓ Ro5	✓ Clean	`Nc1nc2c([nH]c(=O)n2[C@@H]2C[C@@H](O)[C@@H](CO)O…`
ZINC12502183	0.667	283.2 Da LogP -2.36 TPSA 159.2	✓ Ro5	✓ Clean	`Nc1nc2c([nH]c(=O)n2[C@H]2C[C@@H](O)[C@@H](CO)O2…`
ZINC12502185	0.667	283.2 Da LogP -2.36 TPSA 159.2	✓ Ro5	✓ Clean	`Nc1nc2c([nH]c(=O)n2[C@@H]2C[C@H](O)[C@@H](CO)O2…`
ZINC16051666	0.667	283.2 Da LogP -2.36 TPSA 159.2	✓ Ro5	✓ Clean	`Nc1nc2c([nH]c(=O)n2[C@H]2C[C@H](O)[C@@H](CO)O2)…`
ZINC2510814	0.667	283.2 Da LogP -2.36 TPSA 159.2	✓ Ro5	✓ Clean	`Nc1nc2c([nH]c(=O)n2[C@@H]2C[C@@H](O)[C@H](CO)O2…`
ZINC4533532	0.667	283.2 Da LogP -2.36 TPSA 159.2	✓ Ro5	✓ Clean	`Nc1nc2c([nH]c(=O)n2[C@@H]2C[C@H](O)[C@H](CO)O2)…`
ZINC71404870	0.657	230.3 Da LogP 4.23 TPSA 26.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/COP(C)(C)=O`
ZINC8436838	0.657	262.1 Da LogP 0.15 TPSA 133.5	✓ Ro5	✓ Clean	`C/C(=C\CO[P@@](=O)(O)OP(=O)(O)O)CO`
ZINC13539354	0.632	332.2 Da LogP 3.20 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C(\F)CO[P@](=O)(O)OP(=O)(O)O`
ZINC5811921	0.604	333.2 Da LogP -0.94 TPSA 159.5	✓ Ro5	✓ Clean	`NC(=O)c1cccc([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…`
ZINC5811924	0.604	333.2 Da LogP -0.94 TPSA 159.5	✓ Ro5	✓ Clean	`NC(=O)c1cccc([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC5811925	0.604	333.2 Da LogP -0.94 TPSA 159.5	✓ Ro5	✓ Clean	`NC(=O)c1cccc([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…`
ZINC5811926	0.604	333.2 Da LogP -0.94 TPSA 159.5	✓ Ro5	✓ Clean	`NC(=O)c1cccc([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC12296728	0.597	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@@H](O)[C@@H](COP(=O)(O)O)…`
ZINC13527599	0.597	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@@H](O)[C@@H](COP(=O)(O)O…`
ZINC13527603	0.597	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@@H](COP(=O)(O)O)…`
ZINC3869846	0.597	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@H](COP(=O)(O)O)O…`
ZINC3869847	0.597	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2…`

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.