NPASS Compound

Structure

NPC87653 OpenBabel06302215282D 49 53 0 0 1 0 0 0 0 0999 V2000 6.9282 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7994 -3.8249 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.2116 -4.6339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7994 -5.4429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7505 -5.1339 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 3.7015 -5.4429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2893 -4.6339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7015 -3.8249 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7505 -4.1339 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.0622 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 49 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 15 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 37 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 9 15 1 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 12 14 1 0 0 0 0 15 16 1 0 0 0 0 17 16 1 1 0 0 0 17 18 1 0 0 0 0 17 22 1 0 0 0 0 18 19 1 0 0 0 0 18 25 1 6 0 0 0 19 20 1 0 0 0 0 19 24 1 1 0 0 0 20 21 1 0 0 0 0 20 23 1 1 0 0 0 21 22 1 0 0 0 0 26 25 1 1 0 0 0 26 27 1 0 0 0 0 26 33 1 0 0 0 0 27 28 1 0 0 0 0 27 36 1 6 0 0 0 28 29 1 0 0 0 0 28 35 1 1 0 0 0 29 30 1 0 0 0 0 29 34 1 6 0 0 0 30 31 1 1 0 0 0 30 33 1 0 0 0 0 31 32 1 0 0 0 0 37 38 2 0 0 0 0 37 39 1 0 0 0 0 39 40 1 0 0 0 0 41 40 1 6 0 0 0 41 42 1 0 0 0 0 41 48 1 0 0 0 0 42 43 1 0 0 0 0 43 44 1 0 0 0 0 44 48 1 0 0 0 0 44 45 1 0 0 0 0 45 46 1 0 0 0 0 46 47 1 0 0 0 0 48 47 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	691.36
Volume:	689.09
LogP:	3.659
LogD:	2.527
LogS:	-3.919
# Rotatable Bonds:	13
TPSA:	187.84
# H-Bond Aceptor:	13
# H-Bond Donor:	6
# Rings:	5
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.135
Synthetic Accessibility Score:	5.193
Fsp3:	0.694
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.708
MDCK Permeability:	3.399783236091025e-05
Pgp-inhibitor:	0.958
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.969
20% Bioavailability (F20%):	0.01
30% Bioavailability (F30%):	0.915

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.064
Plasma Protein Binding (PPB):	65.59374237060547%
Volume Distribution (VD):	0.567
Pgp-substrate:	17.76752471923828%

ADMET: Metabolism

CYP1A2-inhibitor:	0.018
CYP1A2-substrate:	0.053
CYP2C19-inhibitor:	0.007
CYP2C19-substrate:	0.183
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.033
CYP2D6-inhibitor:	0.925
CYP2D6-substrate:	0.183
CYP3A4-inhibitor:	0.012
CYP3A4-substrate:	0.127

ADMET: Excretion

Clearance (CL):	3.675
Half-life (T1/2):	0.581

ADMET: Toxicity

hERG Blockers:	0.576
Human Hepatotoxicity (H-HT):	0.273
Drug-inuced Liver Injury (DILI):	0.03
AMES Toxicity:	0.048
Rat Oral Acute Toxicity:	0.02
Maximum Recommended Daily Dose:	0.03
Skin Sensitization:	0.596
Carcinogencity:	0.089
Eye Corrosion:	0.003
Eye Irritation:	0.008
Respiratory Toxicity:	0.202

Download Data

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

Natural Product: NPC87653

Natural Product ID:	NPC87653
*Common Name:**	UUYBNFMMBCGDGF-PWHYGFEJSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	UUYBNFMMBCGDGF-PWHYGFEJSA-N
Standard InCHI:	InChI=1S/C36H53NO12/c1-19(2)7-9-21-14-24(34(44)45-17-23-11-13-37-12-5-6-25(23)37)15-22(10-8-20(3)4)32(21)48-36-33(28(40)26(39)18-46-36)49-35-31(43)30(42)29(41)27(16-38)47-35/h7-8,14-15,23,25-31,33,35-36,38-43H,5-6,9-13,16-18H2,1-4H3/t23-,25+,26+,27-,28+,29-,30+,31-,33-,35+,36+/m1/s1
SMILES:	CC(=CCc1cc(cc(CC=C(C)C)c1O[C@H]1[C@@H]([C@H]([C@H](CO1)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)C(=O)OC[C@H]1CCN2CCC[C@@H]12)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	72698098
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0004165] Phenolic glycosides

*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
NPO2364	Cornus florida	Species	Cornaceae	Eukaryota	leaves	Timber Lake, Oxford, Mississippi	2011	PMID[25141901]
NPO2364	Cornus florida	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25141901]
NPO2524	Liparis nervosa	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1765	Cirsium lineare	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10516	Lactarius piperatus	Species	Russulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2524	Liparis nervosa	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22902.1	Alnus alnobetula subsp. crispa	Subspecies	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1765	Cirsium lineare	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25057	Vespertilio sinensis	Species	Vespertilionidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10516	Lactarius piperatus	Species	Russulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2524	Liparis nervosa	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO6397	Schefflera rhododendrifolia	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15943	Chicoreus nobilis	Species	Muricidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5803	Sedum takesimense	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10516	Lactarius piperatus	Species	Russulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1435	Staehelina dubia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7420	Tetraneuris linearifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6778	Suriana maritima	Species	Surianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2222	Litsea wightiana	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8980	Teucrium corymbosum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25057	Vespertilio sinensis	Species	Vespertilionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4270	Cousinia piptocephala	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9372	Hypericum yezoense	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2364	Cornus florida	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3483	Bencomia caudata	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7983	Bassia latifolia	Species	Abylidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1075	Streptomyces natalensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO2524	Liparis nervosa	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7299	Swartzia laevicarpa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO980	Hedera taurica	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22902.1	Alnus alnobetula subsp. crispa	Subspecies	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1765	Cirsium lineare	Species	Asteraceae	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 NPC87653 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	245
0.1-0.2	1023
0.2-0.3	2654
0.3-0.4	7269
0.4-0.5	11450
0.5-0.6	8588
0.6-0.7	10447
0.7-0.8	1021
0.8-0.85	0
0.85-0.9	0
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 NPC87653 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	169
0.1-0.2	520
0.2-0.3	1155
0.3-0.4	2287
0.4-0.5	2681
0.5-0.6	1619
0.6-0.7	660
0.7-0.8	59
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

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