NPASS Compound

Structure

NPC19032 OpenBabel06302215512D 51 52 0 0 1 0 0 0 0 0999 V2000 3.4641 2.0000 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 0.5000 0.0000 C 0 0 0 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 2.5981 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 2 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 -0.0000 2.0000 0.0000 C 0 0 0 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 -0.8660 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.9282 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.9282 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.6603 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.6603 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -10.3923 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -10.3923 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.2583 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.2583 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.1244 2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -12.1244 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.9904 3.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -13.8564 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -13.8564 2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -14.7224 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.9904 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -12.9904 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -13.8564 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 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 -3.4641 2.0000 0.0000 C 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 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 2.0000 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 6.0622 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 5.0000 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 46 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 5 45 1 1 0 0 0 7 6 1 1 0 0 0 7 8 1 0 0 0 0 7 44 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 6 0 0 0 11 44 1 0 0 0 0 13 12 1 1 0 0 0 13 14 1 0 0 0 0 13 42 1 0 0 0 0 14 15 1 1 0 0 0 14 16 1 0 0 0 0 16 17 1 0 0 0 0 16 41 1 6 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 18 40 1 6 0 0 0 19 20 1 6 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 21 39 1 1 0 0 0 22 23 1 1 0 0 0 22 24 1 0 0 0 0 24 25 1 0 0 0 0 24 38 1 6 0 0 0 25 26 1 1 0 0 0 25 27 1 0 0 0 0 27 28 1 0 0 0 0 29 28 1 6 0 0 0 29 30 1 0 0 0 0 29 35 1 0 0 0 0 30 31 1 0 0 0 0 31 32 1 0 0 0 0 31 36 1 1 0 0 0 32 33 1 0 0 0 0 33 34 1 1 0 0 0 33 35 1 0 0 0 0 36 37 1 0 0 0 0 42 43 1 0 0 0 0 46 47 2 0 0 0 0 47 48 1 0 0 0 0 48 49 2 0 0 0 0 48 50 1 0 0 0 0 50 51 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	726.49
Volume:	769.43
LogP:	4.232
LogD:	3.496
LogS:	-4.027
# Rotatable Bonds:	23
TPSA:	164.37
# H-Bond Aceptor:	11
# H-Bond Donor:	5
# Rings:	2
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.046
Synthetic Accessibility Score:	6.03
Fsp3:	0.825
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:	-4.967
MDCK Permeability:	0.00010607361036818475
Pgp-inhibitor:	0.998
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.603
20% Bioavailability (F20%):	0.007
30% Bioavailability (F30%):	0.621

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.028
Plasma Protein Binding (PPB):	62.604331970214844%
Volume Distribution (VD):	0.918
Pgp-substrate:	9.159839630126953%

ADMET: Metabolism

CYP1A2-inhibitor:	0.002
CYP1A2-substrate:	0.138
CYP2C19-inhibitor:	0.003
CYP2C19-substrate:	0.88
CYP2C9-inhibitor:	0.001
CYP2C9-substrate:	0.01
CYP2D6-inhibitor:	0.0
CYP2D6-substrate:	0.069
CYP3A4-inhibitor:	0.433
CYP3A4-substrate:	0.734

ADMET: Excretion

Clearance (CL):	5.503
Half-life (T1/2):	0.499

ADMET: Toxicity

hERG Blockers:	0.401
Human Hepatotoxicity (H-HT):	0.827
Drug-inuced Liver Injury (DILI):	0.003
AMES Toxicity:	0.133
Rat Oral Acute Toxicity:	0.008
Maximum Recommended Daily Dose:	0.992
Skin Sensitization:	0.976
Carcinogencity:	0.279
Eye Corrosion:	0.004
Eye Irritation:	0.015
Respiratory Toxicity:	0.957

Download Data

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

Natural Product: NPC19032

Natural Product ID:	NPC19032
*Common Name:**	PRFYUYVIJXVABS-YJMSTTENSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PRFYUYVIJXVABS-YJMSTTENSA-N
Standard InCHI:	InChI=1S/C40H70O11/c1-24(14-18-38(44)49-9)13-16-30(41)20-31-11-10-12-32(51-31)22-37(48-8)27(4)35(42)23-36(43)28(5)40(46)29(6)39(45)25(2)15-17-33-21-34(47-7)19-26(3)50-33/h10-11,13-14,18,25-37,39-43,45-46H,12,15-17,19-23H2,1-9H3/b18-14+,24-13+/t25-,26-,27-,28-,29-,30-,31-,32-,33-,34+,35-,36+,37-,39-,40-/m0/s1
SMILES:	C/C(=CC[C@@H](C[C@@H]1C=CC[C@@H](C[C@@H]([C@@H](C)[C@H](C[C@H]([C@H](C)[C@@H]([C@@H](C)[C@H]([C@@H](C)CC[C@H]2C[C@@H](C[C@H](C)O2)OC)O)O)O)O)OC)O1)O)/C=C/C(=O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11967032
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001755] Diterpene 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
NPO11713	Hypericum scabrum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15568778]
NPO11713	Hypericum scabrum	Species	Hypericaceae	Eukaryota	n.a.	Uzbekistan	n.a.	PMID[15568778]
NPO11171	Stelletta clavosa	Species	Ancorinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[21280591]
NPO16259	Syringa reticulata	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21955940]
NPO11713	Hypericum scabrum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27280968]
NPO18739	Exallage chrysotricha	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12904	Nauclea coadunata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18739	Exallage chrysotricha	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9400	Mutisia homoeantha	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11025	Cryptocarya leucophylla	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14193	Pleiococca wilcoxiana	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO11879	Polistes rothneyi	Species	Vespidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6693	Streptomyces triangulatus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO1444	Thalictrum amurense	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16259	Syringa reticulata	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25737	Solanum pimpinellifolium	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13207	Leptoclinides durus	Species	Didemnidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11713	Hypericum scabrum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11171	Stelletta clavosa	Species	Ancorinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6855	Chaenostoma foetidum	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7014	Retaster insignis	n.a.	n.a.	n.a.	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 NPC19032 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	165
0.1-0.2	935
0.2-0.3	3989
0.3-0.4	7825
0.4-0.5	16186
0.5-0.6	8962
0.6-0.7	3895
0.7-0.8	670
0.8-0.85	38
0.85-0.9	15
0.9-0.95	17
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 NPC19032 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	147
0.1-0.2	1126
0.2-0.3	3564
0.3-0.4	2690
0.4-0.5	1240
0.5-0.6	300
0.6-0.7	69
0.7-0.8	12
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