NPASS Compound

Natural Product: NPC328660

Natural Product ID	NPC328660
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	ZUGFBNMTMJLCQZ-MACXSXHHSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	44223978
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000289] Nucleosides, nucleotides, and analogues [CHEMONTID:0001506] Purine nucleotides [CHEMONTID:0001544] Purine ribonucleotides [CHEMONTID:0001617] Purine ribonucleoside monophosphates

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 47 49 0 0 0 0 0 0 0 0999 V2000 -3.6283 -3.9248 0.3872 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8012 -2.4522 0.0985 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5944 -1.9544 -0.6104 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2730 -2.5325 -1.7035 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8118 -0.9107 -0.1530 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6993 -0.5298 -0.9057 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6544 0.9381 -1.2105 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5279 1.4463 -0.7185 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4208 0.4108 -0.7932 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6137 -0.7176 -0.1363 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3640 -0.3942 1.1814 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6547 0.6570 -0.0846 N 0 0 0 0 0 0 0 0 0 0 0 0 2.9336 1.5187 0.8920 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2291 1.3895 1.2432 N 0 0 0 0 0 0 0 0 0 0 0 0 4.7994 0.4365 0.4900 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0788 -0.1146 0.4077 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3096 -1.0912 -0.4955 N 0 0 0 0 0 0 0 0 0 0 0 0 5.3436 -1.5279 -1.2974 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1317 -0.9951 -1.2085 N 0 0 0 0 0 0 0 0 0 0 0 0 3.7904 -0.0178 -0.3455 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0762 0.3761 1.2759 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.8707 1.6587 -0.6791 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7832 2.9961 -1.0474 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0947 3.8956 -0.5030 P 0 0 0 0 0 0 0 0 0 0 0 0 -3.4884 4.8648 -1.5674 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4044 2.9120 -0.0851 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5757 4.7712 0.8585 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0047 -1.6882 1.2961 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.1797 -4.0615 1.3913 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5796 -4.4464 0.2556 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9027 -4.3284 -0.3621 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6811 -2.3548 -0.5810 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5818 -1.1510 -1.8267 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6746 1.0480 -2.3161 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5585 0.1142 -1.8363 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0571 -1.6968 -0.2989 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4711 -0.8303 1.4633 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1922 2.2049 1.3112 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4867 -2.3153 -2.0416 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7611 -0.2731 1.6874 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1132 1.3824 1.4931 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9660 1.5673 0.4065 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7576 1.2047 -1.1654 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3852 2.6522 0.8707 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3942 4.9825 1.3879 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6146 -0.8612 1.0306 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5698 -2.2579 1.9893 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 3 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 9 12 1 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 16 21 1 0 7 22 1 0 22 23 1 0 23 24 1 0 24 25 2 0 24 26 1 0 24 27 1 0 2 28 1 0 10 6 1 0 20 12 1 0 20 15 1 0 1 29 1 0 1 30 1 0 1 31 1 0 2 32 1 0 6 33 1 0 7 34 1 0 9 35 1 0 10 36 1 0 11 37 1 0 13 38 1 0 18 39 1 0 21 40 1 0 21 41 1 0 22 42 1 0 22 43 1 0 26 44 1 0 27 45 1 0 28 46 1 0 28 47 1 0 M END

Standard InCHIKey	ZUGFBNMTMJLCQZ-MACXSXHHSA-N
Standard InCHI	InChI=1S/C13H19N6O8P/c1-5(14)13(21)27-9-6(2-25-28(22,23)24)26-12(8(9)20)19-4-18-7-10(15)16-3-17-11(7)19/h3-6,8-9,12,20H,2,14H2,1H3,(H2,15,16,17)(H2,22,23,24)/t5-,6+,8+,9+,12+/m0/s1
SMILES	CC(C(=O)OC1C(OC(C1O)N2C=NC3=C(N=CN=C32)N)COP(=O)(O)O)N

Calculated Properties

Physi-Chem Properties

Molecular Weight:	418.1	Volume:	350.682 ? Van der Waals volume.
Dense:	1.192	LogP:	-2.011 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-0.076 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.678 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	7.0	Rigid Bonds:	17.0
TPSA:	218.16 ? Topological Polar Surface Area.	H-Bond Acceptor:	14.0
H-Bond Donor:	7.0	Rings:	3.0
Heavy Atoms:	15.0

MedChem Properties

QED Drug-Likeness Score:	0.254	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.154	Fsp³:	0.538
MCE-18:	74.8 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	1	PAINS Alert:	0
Colloidal aggregators:	0.093	Fluc inhibitor:	0.003 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.011 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.023 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.049	Promiscuous compounds:	0.022

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.799	MDCK Permeability:	-5.343
Pgp-inhibitor:	0.0	Pgp-substrate:	0.002
PAMPA:	0.991 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.0	30% Bioavailability (F30%):	0.0
50% Bioavailability (F50%):	0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.814
Plasma Protein Binding (PPB):	20.146%	Volume Distribution (VD):	-0.375
Fu:	76.705% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.783
OATP1B3 inhibitor:	0.999	BCRP inhibitor:	0.0
BSEP inhibitor:	0.246

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.001	CYP2C9-substrate:	0.006
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.002
HLM stability:	0.999 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

2.452

Half-life (T1/2):

1.882

ADMET: Toxicity

hERG Blockers:	0.032	hERG Blockers (10um):	0.071
Human Hepatotoxicity (H-HT):	0.629	Drug-induced Liver Injury (DILI):	0.877
AMES Toxicity:	0.282	Rat Oral Acute Toxicity:	0.158
Maximum Recommended Daily Dose:	0.972	Skin Sensitization:	0.37
Carcinogencity:	0.673	Eye Corrosion:	0.0
Eye Irritation:	0.018	Respiratory Toxicity:	0.977
Drug-induced Neurotoxicity:	0.898	Ototoxicity:	0.84
Hematotoxicity:	0.158	Drug-induced Nephrotoxicity:	0.981
Genotoxicity:	1.0	RPMI-8226 Immunitoxicity:	0.156
A549 Cytotoxicity:	0.004	Hek293 Cytotoxicity:	0.32
BCF:	0.077 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	2.444 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	3.839 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.369 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO30193	Mycoplasma genitalium	Species	Mycoplasmataceae	Bacteria	n.a.	n.a.	n.a.	PMID[22817898]
NPO30193	Mycoplasma genitalium	Species	Mycoplasmataceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	Organism Name	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC328660 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	25060
0.1-0.2	24621
0.2-0.3	75
0.3-0.4	39
0.4-0.5	31
0.5-0.6	25
0.6-0.7	6
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8088	Intermediate Similarity	NPC164952
0.6986	Remote Similarity	NPC302778
0.6986	Remote Similarity	NPC329404
0.6986	Remote Similarity	NPC212551
0.6528	Remote Similarity	NPC85689
0.6351	Remote Similarity	NPC185991
0.6351	Remote Similarity	NPC321814
0.5844	Remote Similarity	NPC121222
0.575	Remote Similarity	NPC130586
0.561	Remote Similarity	NPC174802
0.5571	Remote Similarity	NPC317821
0.5542	Remote Similarity	NPC481375
0.5542	Remote Similarity	NPC606410
0.5432	Remote Similarity	NPC324198
0.5432	Remote Similarity	NPC326529
0.5432	Remote Similarity	NPC319100
0.54	Remote Similarity	NPC189261
0.5263	Remote Similarity	NPC136349
0.5263	Remote Similarity	NPC219313
0.5256	Remote Similarity	NPC211025
0.5222	Remote Similarity	NPC326082
0.5205	Remote Similarity	NPC156461
0.5205	Remote Similarity	NPC107374
0.5205	Remote Similarity	NPC600382
0.5205	Remote Similarity	NPC612067
0.5176	Remote Similarity	NPC161224
0.5135	Remote Similarity	NPC229974
0.5116	Remote Similarity	NPC316618
0.5116	Remote Similarity	NPC323091
0.5067	Remote Similarity	NPC609472
0.5062	Remote Similarity	NPC328479
0.506	Remote Similarity	NPC224076

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC328660 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5285
0.1-0.2	3716
0.2-0.3	80
0.3-0.4	49
0.4-0.5	12
0.5-0.6	7
0.6-0.7	1
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.6351	Remote Similarity	NPD283	Phase 4
0.561	Remote Similarity	NPD339	Phase 2
0.5263	Remote Similarity	NPD548	Clinical (unspecified phase)
0.5205	Remote Similarity	NPD249	Phase 4
0.5205	Remote Similarity	NPD250	Phase 4
0.5185	Remote Similarity	NPD4171	Clinical (unspecified phase)
0.506	Remote Similarity	NPD169	Phase 2
0.506	Remote Similarity	NPD338	Approved

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data