NPASS Compound

Structure

NPC124304 OpenBabel06302215312D 44 47 0 0 1 0 0 0 0 0999 V2000 -6.9282 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.7942 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.7942 -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 -6.0622 -0.5000 0.0000 C 0 0 1 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 -5.1962 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4641 -2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -3.5000 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 -3.4641 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -5.0000 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 -6.0622 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -6.5000 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 -2.5981 -0.5000 0.0000 C 0 0 2 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 O 0 0 0 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 O 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 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 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 0.0000 1.0000 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 1.7321 1.0000 0.0000 C 0 0 0 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 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 0.8660 -1.5000 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 -5.1962 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 1.0000 0.0000 O 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 -8.6603 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 7 1 0 0 0 0 3 4 1 0 0 0 0 3 44 1 6 0 0 0 4 5 1 0 0 0 0 4 43 1 1 0 0 0 5 6 1 0 0 0 0 5 42 1 1 0 0 0 6 7 1 0 0 0 0 6 8 1 6 0 0 0 9 8 1 6 0 0 0 9 10 1 0 0 0 0 9 27 1 0 0 0 0 10 11 1 0 0 0 0 10 41 1 1 0 0 0 11 12 1 1 0 0 0 11 23 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 20 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 18 22 1 0 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 1 0 0 0 24 27 1 0 0 0 0 25 26 1 0 0 0 0 27 28 1 6 0 0 0 28 29 1 0 0 0 0 29 30 2 0 0 0 0 29 31 1 0 0 0 0 31 32 2 0 0 0 0 32 33 1 0 0 0 0 33 38 2 0 0 0 0 33 34 1 0 0 0 0 34 35 2 0 0 0 0 35 36 1 0 0 0 0 36 37 2 0 0 0 0 36 40 1 0 0 0 0 37 38 1 0 0 0 0 37 39 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	624.21
Volume:	586.676
LogP:	0.649
LogD:	0.007
LogS:	-2.226
# Rotatable Bonds:	11
TPSA:	245.29
# H-Bond Aceptor:	15
# H-Bond Donor:	9
# Rings:	4
# Heavy Atoms:	15

MedChem Properties

QED Drug-Likeness Score:	0.087
Synthetic Accessibility Score:	4.727
Fsp3:	0.483
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.574
MDCK Permeability:	2.913577191065997e-05
Pgp-inhibitor:	0.007
Pgp-substrate:	0.989
Human Intestinal Absorption (HIA):	0.991
20% Bioavailability (F20%):	0.501
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.075
Plasma Protein Binding (PPB):	94.92569732666016%
Volume Distribution (VD):	0.297
Pgp-substrate:	7.143305778503418%

ADMET: Metabolism

CYP1A2-inhibitor:	0.078
CYP1A2-substrate:	0.017
CYP2C19-inhibitor:	0.091
CYP2C19-substrate:	0.052
CYP2C9-inhibitor:	0.131
CYP2C9-substrate:	0.223
CYP2D6-inhibitor:	0.047
CYP2D6-substrate:	0.163
CYP3A4-inhibitor:	0.074
CYP3A4-substrate:	0.023

ADMET: Excretion

Clearance (CL):	2.257
Half-life (T1/2):	0.874

ADMET: Toxicity

hERG Blockers:	0.082
Human Hepatotoxicity (H-HT):	0.133
Drug-inuced Liver Injury (DILI):	0.136
AMES Toxicity:	0.511
Rat Oral Acute Toxicity:	0.111
Maximum Recommended Daily Dose:	0.005
Skin Sensitization:	0.967
Carcinogencity:	0.051
Eye Corrosion:	0.003
Eye Irritation:	0.056
Respiratory Toxicity:	0.027

Download Data

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

Natural Product: NPC124304

Natural Product ID:	NPC124304
*Common Name:**	FBSKJMQYURKNSU-FPASGECCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	FBSKJMQYURKNSU-FPASGECCSA-N
Standard InCHI:	InChI=1S/C29H36O15/c1-13-22(36)23(37)24(38)29(41-13)44-27-25(39)28(40-9-8-15-3-6-17(32)19(34)11-15)42-20(12-30)26(27)43-21(35)7-4-14-2-5-16(31)18(33)10-14/h2-7,10-11,13,20,22-34,36-39H,8-9,12H2,1H3/b7-4+/t13-,20+,22-,23+,24+,25-,26+,27-,28+,29-/m0/s1
SMILES:	C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@H]1[C@@H]([C@H](OCCc2ccc(c(c2)O)O)O[C@H](CO)[C@H]1OC(=O)/C=C/c1ccc(c(c1)O)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:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000476] Cinnamic acids and derivatives [CHEMONTID:0001391] Hydroxycinnamic acids and derivatives [CHEMONTID:0000059] Coumaric acids and derivatives

*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
NPO12373	Vinca minor	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10011	Myrsine capitellata	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7135	Mollugo spergula	Species	Molluginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6413	Viguiera stenoloba	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12373	Vinca minor	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10011	Myrsine capitellata	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5805	Chlorociboria aeruginascens	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12241	Hypericum reflexum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6864	Lactarius spinosulus	Species	Russulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12373	Vinca minor	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6413	Viguiera stenoloba	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11342	Sideritis trojana	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9162	Nicotiana affinis	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11625	Markhamia stipulata	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13327	Phomopsis leptostromiformis	Species	Valsaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO944	Senecio sandersonii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12598	Osteospermum fruticosum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7135	Mollugo spergula	Species	Molluginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15456	Sideritis soluta	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10011	Myrsine capitellata	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2471	Axinyssa variabilis	Species	Halichondriidae	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 NPC124304 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	301
0.1-0.2	1303
0.2-0.3	3109
0.3-0.4	7603
0.4-0.5	10013
0.5-0.6	7802
0.6-0.7	8593
0.7-0.8	3443
0.8-0.85	332
0.85-0.9	109
0.9-0.95	66
0.95-1	23

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 NPC124304 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	254
0.1-0.2	777
0.2-0.3	1611
0.3-0.4	2910
0.4-0.5	2002
0.5-0.6	1184
0.6-0.7	369
0.7-0.8	41
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	1

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