NPASS Compound

Structure

NPC32877 OpenBabel06302215112D 59 64 0 0 1 0 0 0 0 0999 V2000 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 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 1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 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 3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 O 0 3 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 -0.0000 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 2 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 -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 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 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 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 3.5000 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 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 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.9282 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.9282 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.7942 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 0.5000 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 -10.3923 0.0000 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 O 0 0 0 0 0 0 0 0 0 0 0 0 -12.1244 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 0.5000 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 -2.5000 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 -6.0622 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.0000 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 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 2.5981 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 59 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 3 0 0 0 8 9 1 0 0 0 0 9 10 2 3 0 0 0 9 58 1 0 0 0 0 10 11 1 0 0 0 0 12 11 1 6 0 0 0 12 13 1 0 0 0 0 12 54 1 0 0 0 0 13 14 1 0 0 0 0 13 57 1 1 0 0 0 14 15 1 0 0 0 0 14 56 1 6 0 0 0 15 16 1 0 0 0 0 15 55 1 1 0 0 0 16 17 1 6 0 0 0 16 54 1 0 0 0 0 17 18 1 0 0 0 0 18 46 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 20 25 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 21 45 1 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 23 44 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 27 26 1 1 0 0 0 27 28 1 0 0 0 0 27 40 1 0 0 0 0 28 29 1 0 0 0 0 28 43 1 6 0 0 0 29 30 1 0 0 0 0 29 42 1 1 0 0 0 30 31 1 0 0 0 0 30 41 1 6 0 0 0 31 32 1 1 0 0 0 31 40 1 0 0 0 0 32 33 1 0 0 0 0 33 34 1 0 0 0 0 34 35 2 0 0 0 0 34 36 1 0 0 0 0 36 37 1 0 0 0 0 37 38 2 0 0 0 0 37 39 1 0 0 0 0 45 46 1 0 0 0 0 46 47 2 3 0 0 0 47 53 1 0 0 0 0 47 48 1 0 0 0 0 48 49 2 0 0 0 0 49 50 1 0 0 0 0 50 51 2 0 0 0 0 50 52 1 0 0 0 0 52 53 2 0 0 0 0 M CHG 1 10 1 M END $$$$

Physi-Chem Properties

Molecular Weight:	827.2
Volume:	769.337
LogP:	1.12
LogD:	0.183
LogS:	-4.166
# Rotatable Bonds:	15
TPSA:	323.2
# H-Bond Aceptor:	20
# H-Bond Donor:	10
# Rings:	6
# Heavy Atoms:	20

MedChem Properties

QED Drug-Likeness Score:	0.035
Synthetic Accessibility Score:	5.503
Fsp3:	0.333
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	2
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.818
MDCK Permeability:	4.3017960706492886e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.927
20% Bioavailability (F20%):	0.733
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.063
Plasma Protein Binding (PPB):	92.42513275146484%
Volume Distribution (VD):	0.63
Pgp-substrate:	5.278494834899902%

ADMET: Metabolism

CYP1A2-inhibitor:	0.091
CYP1A2-substrate:	0.005
CYP2C19-inhibitor:	0.044
CYP2C19-substrate:	0.039
CYP2C9-inhibitor:	0.033
CYP2C9-substrate:	0.592
CYP2D6-inhibitor:	0.031
CYP2D6-substrate:	0.102
CYP3A4-inhibitor:	0.055
CYP3A4-substrate:	0.006

ADMET: Excretion

Clearance (CL):	1.346
Half-life (T1/2):	0.914

ADMET: Toxicity

hERG Blockers:	0.174
Human Hepatotoxicity (H-HT):	0.188
Drug-inuced Liver Injury (DILI):	0.98
AMES Toxicity:	0.513
Rat Oral Acute Toxicity:	0.066
Maximum Recommended Daily Dose:	0.002
Skin Sensitization:	0.227
Carcinogencity:	0.157
Eye Corrosion:	0.003
Eye Irritation:	0.024
Respiratory Toxicity:	0.006

Download Data

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

Natural Product: NPC32877

Natural Product ID:	NPC32877
*Common Name:**	SVWGZAOFZPHNJL-KMKFZPLVSA-O
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SVWGZAOFZPHNJL-KMKFZPLVSA-O
Standard InCHI:	InChI=1S/C39H38O20/c40-19-6-1-17(2-7-19)3-10-29(45)53-15-26-31(47)34(50)36(52)39(59-26)57-25-13-22-23(55-37(25)18-4-8-20(41)9-5-18)11-21(42)12-24(22)56-38-35(51)33(49)32(48)27(58-38)16-54-30(46)14-28(43)44/h1-13,26-27,31-36,38-39,47-52H,14-16H2,(H3-,40,41,42,43,44,45)/p+1/t26-,27-,31-,32-,33+,34+,35-,36-,38-,39-/m1/s1
SMILES:	c1cc(ccc1C=CC(=[O+]C[C@@H]1[C@H]([C@@H]([C@H]([C@H](OC2=Cc3c(cc(cc3O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](COC(=O)CC(=O)O)O3)O)O)O)O)OC2=C2C=CC(=O)C=C2)O1)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
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
NPO1524	Rosa rugosa	Species	Rosaceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.1016/j.foodcont.2014.02.001]
NPO9130	Phyllospongia papyracea	Species	Thorectidae	Eukaryota	n.a.	Papua New Guinea, at depths of 60 ft (914948? S, 15046808? E)	n.a.	PMID[17455979]
NPO9130	Phyllospongia papyracea	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	PMID[17455979]
NPO1524	Rosa rugosa	Species	Rosaceae	Eukaryota	Flowers	n.a.	n.a.	PMID[20467822]
NPO1524	Rosa rugosa	Species	Rosaceae	Eukaryota	flower buds	n.a.	n.a.	PMID[24063567]
NPO1524	Rosa rugosa	Species	Rosaceae	Eukaryota	Roots	n.a.	n.a.	PMID[24461297]
NPO18491	Hyacinthus orientalis	Species	Hyacinthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9599261]
NPO27293	Sus scrofa	Species	Suidae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO17260	Xanthosoma sagittifolium	Species	Araceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO17260	Xanthosoma sagittifolium	Species	Araceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO17260	Xanthosoma sagittifolium	Species	Araceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO18491	Hyacinthus orientalis	Species	Hyacinthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4156	Apocynum androsaemifolium	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19982	Crotalaria sessiliflora	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1524	Rosa rugosa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13822	Aconitum fischeri	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19982	Crotalaria sessiliflora	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1524	Rosa rugosa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4156	Apocynum androsaemifolium	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27293	Sus scrofa	Species	Suidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18491	Hyacinthus orientalis	Species	Hyacinthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13822	Aconitum fischeri	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4156	Apocynum androsaemifolium	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1524	Rosa rugosa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO13822	Aconitum fischeri	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1524	Rosa rugosa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO27293	Sus scrofa	Species	Suidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18743	Lagascea mollis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19349	Phlegmariurus yunnanensis	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9130	Phyllospongia papyracea	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6288	Talaromyces islandicus	Species	Trichocomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11751	Tetracera alnifolia	Species	Dilleniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13822	Aconitum fischeri	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19066	Pisolithus arhizus	Species	Pisolithaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17260	Xanthosoma sagittifolium	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18982	Espeletia grandiflora	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18491	Hyacinthus orientalis	Species	Hyacinthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1524	Rosa rugosa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17182	Pulmonaria mollis	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4156	Apocynum androsaemifolium	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19982	Crotalaria sessiliflora	Species	Fabaceae	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 NPC32877 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	357
0.1-0.2	1601
0.2-0.3	4008
0.3-0.4	9092
0.4-0.5	9092
0.5-0.6	5611
0.6-0.7	7509
0.7-0.8	4722
0.8-0.85	645
0.85-0.9	60
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 NPC32877 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	306
0.1-0.2	860
0.2-0.3	1930
0.3-0.4	2820
0.4-0.5	1832
0.5-0.6	1004
0.6-0.7	317
0.7-0.8	72
0.8-0.85	9
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