NPASS Compound

Structure

NPC190904 OpenBabel06302215432D 40 46 0 0 1 0 0 0 0 0999 V2000 5.1513 -3.3309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6513 -4.1970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6732 -3.9890 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5686 -2.9945 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.4822 -2.5878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7026 -2.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7026 -1.4945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8366 -2.9945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8366 -3.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9706 -4.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1045 -3.9945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7615 -4.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7615 -5.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6275 -5.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4935 -5.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4935 -4.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6275 -3.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4446 -4.1855 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0324 -4.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4446 -5.8035 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1045 -2.9945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7615 -2.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6275 -2.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4935 -2.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3596 -2.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2256 -2.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2256 -1.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3596 -0.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4935 -1.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5675 -0.0164 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5620 0.0882 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9687 -0.8254 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9706 -2.4945 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9706 -1.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8366 -0.9945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1045 -0.9945 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.8090 -1.4013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4781 -0.6581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9781 0.2079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 5 1 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 4 6 1 0 0 0 0 6 7 2 0 0 0 0 8 6 1 1 0 0 0 8 9 1 0 0 0 0 8 33 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 11 12 1 1 0 0 0 11 21 1 0 0 0 0 12 17 2 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 15 20 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 21 22 1 1 0 0 0 21 33 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 24 29 2 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 26 27 1 0 0 0 0 27 32 1 0 0 0 0 27 28 2 0 0 0 0 28 29 1 0 0 0 0 28 30 1 0 0 0 0 30 31 1 0 0 0 0 31 32 1 0 0 0 0 33 34 1 6 0 0 0 34 35 2 0 0 0 0 34 36 1 0 0 0 0 36 40 1 0 0 0 0 36 37 1 0 0 0 0 37 38 1 0 0 0 0 38 39 1 0 0 0 0 39 40 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	542.24
Volume:	550.503
LogP:	5.095
LogD:	3.709
LogS:	-4.604
# Rotatable Bonds:	6
TPSA:	83.86
# H-Bond Aceptor:	8
# H-Bond Donor:	2
# Rings:	7
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.489
Synthetic Accessibility Score:	3.706
Fsp3:	0.375
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.077
MDCK Permeability:	2.8801079679396935e-05
Pgp-inhibitor:	0.641
Pgp-substrate:	0.146
Human Intestinal Absorption (HIA):	0.001
20% Bioavailability (F20%):	0.005
30% Bioavailability (F30%):	0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.27
Plasma Protein Binding (PPB):	98.67376708984375%
Volume Distribution (VD):	1.664
Pgp-substrate:	1.3065228462219238%

ADMET: Metabolism

CYP1A2-inhibitor:	0.911
CYP1A2-substrate:	0.163
CYP2C19-inhibitor:	0.608
CYP2C19-substrate:	0.352
CYP2C9-inhibitor:	0.07
CYP2C9-substrate:	0.143
CYP2D6-inhibitor:	0.99
CYP2D6-substrate:	0.887
CYP3A4-inhibitor:	0.955
CYP3A4-substrate:	0.347

ADMET: Excretion

Clearance (CL):	11.791
Half-life (T1/2):	0.295

ADMET: Toxicity

hERG Blockers:	0.864
Human Hepatotoxicity (H-HT):	0.473
Drug-inuced Liver Injury (DILI):	0.229
AMES Toxicity:	0.112
Rat Oral Acute Toxicity:	0.038
Maximum Recommended Daily Dose:	0.892
Skin Sensitization:	0.804
Carcinogencity:	0.538
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.927

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC190904

Natural Product ID:	NPC190904
*Common Name:**	DEWJJPMPIRTPPW-JZDZDGRVSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DEWJJPMPIRTPPW-JZDZDGRVSA-N
Standard InCHI:	InChI=1S/C32H34N2O6/c35-31(33-13-1-2-14-33)25-10-9-23(22-7-12-27-29(18-22)40-20-38-27)24(30(25)32(36)34-15-3-4-16-34)8-5-21-6-11-26-28(17-21)39-19-37-26/h5-12,17-18,23-25,30H,1-4,13-16,19-20H2/b8-5+/t23-,24+,25-,30-/m0/s1
SMILES:	C1CCN(C1)C(=O)[C@H]1C=C[C@@H](c2ccc3c(c2)OCO3)[C@@H](/C=C/c2ccc3c(c2)OCO3)[C@@H]1C(=O)N1CCCC1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	102480093
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000296] Benzodioxoles

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO10274	Pothomorphe peltata	n.a.	n.a.	n.a.	n.a.	Dominican Republic	n.a.	PMID[11430019]
NPO6544	Carpesium longifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14695795]
NPO3968	Dracontium loretense	Species	Araceae	Eukaryota	corms	Iquitos, Peru	2005-MAY	PMID[19341262]
NPO3968	Dracontium loretense	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19341262]
NPO10666	Verbesina virginica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19485332]
NPO4251	Photorhabdus luminescens	Species	Morganellaceae	Bacteria	n.a.	n.a.	n.a.	PMID[22909174]
NPO12125	Pseudomonas stutzeri	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[23149469]
NPO6648	Piper retrofractum	Species	Piperaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[23506561]
NPO6648	Piper retrofractum	Species	Piperaceae	Eukaryota	leaves	n.a.	n.a.	PMID[25127165]
NPO4251	Photorhabdus luminescens	Species	Morganellaceae	Bacteria	n.a.	n.a.	n.a.	PMID[25988621]
NPO6544	Carpesium longifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7158	Schefflera venulosa	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6648	Piper retrofractum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6544	Carpesium longifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12383	Frullania brasiliensis	Species	Frullaniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27487	Silene banksia	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7158	Schefflera venulosa	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7536	Mycoplasma mycoides	Species	Mycoplasmataceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO2840	Podocarpus minor	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4251	Photorhabdus luminescens	Species	Morganellaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO964	Homalium laurifolium	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10459	Brickellia longifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9950	Coelogyne nitida	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3968	Dracontium loretense	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10274	Pothomorphe peltata	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO230	Palisota barteri	Species	Commelinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9166	Monascus rubropunctatus	Species	Fellodistomidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11511	Cochlearia officinalis	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO876	Didymosphaeria enalia	Species	Didymosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO43	Leifsonia aquatica	Species	Microbacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO7158	Schefflera venulosa	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12488	Bupleurum rigidum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6880	Crocus corsicus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23642	Penicillium tardum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6648	Piper retrofractum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6544	Carpesium longifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13059	Abies webbiana	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2393	Matsumurella chinensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10666	Verbesina virginica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12125	Pseudomonas stutzeri	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO27487	Silene banksia	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12383	Frullania brasiliensis	Species	Frullaniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6428	Euphorbia wangii	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11137	Dichotomanthes tristaniicarpa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8639	Agaricus xanthodermus	Species	Agaricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ 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	NP ID	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

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

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC190904 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	297
0.1-0.2	1382
0.2-0.3	4321
0.3-0.4	13236
0.4-0.5	6163
0.5-0.6	14181
0.6-0.7	2777
0.7-0.8	327
0.8-0.85	11
0.85-0.9	2
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID

Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC190904 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	190
0.1-0.2	692
0.2-0.3	1006
0.3-0.4	2455
0.4-0.5	2653
0.5-0.6	1670
0.6-0.7	442
0.7-0.8	40
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

Bioactivity similarity: Similar Natural Products in NPASS

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