NPASS Compound

Structure

NPC88481 OpenBabel06302216192D 34 38 0 0 1 0 0 0 0 0999 V2000 2.4733 2.3790 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6497 2.8552 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6503 3.8065 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8256 2.3800 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0017 2.8557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8228 2.3803 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0005 0.9523 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8250 1.4277 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6760 1.9183 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6495 0.9510 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6489 -0.0013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8244 -0.4767 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.8239 -1.4290 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6748 -0.9384 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6481 -1.9051 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6472 -2.8570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8222 -3.3326 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0019 -2.8565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0011 -1.9046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8255 -1.4280 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8250 -0.4757 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7007 0.9833 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8218 -4.3149 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4745 1.4267 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1113 0.7186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8165 -0.1869 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0429 0.9161 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3377 1.8216 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2694 2.0191 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9062 1.3110 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6114 0.4054 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.6797 0.2080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8434 0.4657 0.0000 O 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 4 2 1 6 0 0 0 4 5 1 0 0 0 0 4 8 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 22 1 0 0 0 0 7 8 1 0 0 0 0 7 34 1 6 0 0 0 8 9 1 6 0 0 0 8 10 1 0 0 0 0 10 11 1 0 0 0 0 10 25 1 6 0 0 0 11 12 1 0 0 0 0 12 22 1 0 0 0 0 12 13 1 0 0 0 0 13 19 1 0 0 0 0 13 14 1 6 0 0 0 13 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 17 24 1 6 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 6 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 26 28 1 0 0 0 0 28 33 2 0 0 0 0 28 29 1 0 0 0 0 29 30 2 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 32 33 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	469.25
Volume:	480.685
LogP:	1.764
LogD:	0.925
LogS:	-3.665
# Rotatable Bonds:	4
TPSA:	116.95
# H-Bond Aceptor:	7
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.46
Synthetic Accessibility Score:	4.732
Fsp3:	0.667
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.952
MDCK Permeability:	1.58666316565359e-05
Pgp-inhibitor:	0.003
Pgp-substrate:	0.957
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.963
30% Bioavailability (F30%):	0.103

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.961
Plasma Protein Binding (PPB):	74.65185546875%
Volume Distribution (VD):	1.759
Pgp-substrate:	23.64722442626953%

ADMET: Metabolism

CYP1A2-inhibitor:	0.036
CYP1A2-substrate:	0.572
CYP2C19-inhibitor:	0.275
CYP2C19-substrate:	0.568
CYP2C9-inhibitor:	0.176
CYP2C9-substrate:	0.185
CYP2D6-inhibitor:	0.011
CYP2D6-substrate:	0.14
CYP3A4-inhibitor:	0.834
CYP3A4-substrate:	0.378

ADMET: Excretion

Clearance (CL):	6.467
Half-life (T1/2):	0.532

ADMET: Toxicity

hERG Blockers:	0.042
Human Hepatotoxicity (H-HT):	0.232
Drug-inuced Liver Injury (DILI):	0.082
AMES Toxicity:	0.005
Rat Oral Acute Toxicity:	0.266
Maximum Recommended Daily Dose:	0.941
Skin Sensitization:	0.146
Carcinogencity:	0.836
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.949

Download Data

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

Natural Product: NPC88481

Natural Product ID:	NPC88481
*Common Name:**	OQFVSKGDZKMZEH-QUMGVHPFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	OQFVSKGDZKMZEH-QUMGVHPFSA-N
Standard InCHI:	InChI=1S/C27H35NO6/c1-16(29)20-8-11-27(33)25(20,3)22(34-23(31)17-5-4-12-28-15-17)14-21-24(2)9-7-19(30)13-18(24)6-10-26(21,27)32/h4-6,12,15,19-22,30,32-33H,7-11,13-14H2,1-3H3/t19-,20+,21?,22+,24-,25-,26-,27+/m0/s1
SMILES:	CC(=O)[C@H]1CC[C@]2([C@]1(C)[C@@H](CC1[C@@]3(C)CC[C@@H](CC3=CC[C@@]21O)O)OC(=O)c1cccnc1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	5320138
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0003569] Pregnane steroids [CHEMONTID:0001468] Gluco/mineralocorticoids, progestogins 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
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	fruits	n.a.	n.a.	PMID[12467621]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	n.a.	root	n.a.	PMID[16212233]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	roots	purchased from Kiu Shun Trading Ltd., Vancouver, Canada	2000	PMID[16643021]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	leaf	n.a.	PMID[18409045]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[19757853]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	flower buds	n.a.	n.a.	PMID[19926279]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	root	n.a.	PMID[2092947]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	berry	n.a.	n.a.	PMID[21216145]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[21370894]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	root bark	n.a.	n.a.	PMID[23282106]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	leaves	n.a.	n.a.	PMID[24290061]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24968750]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25152999]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25538068]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	stems-leaves	n.a.	n.a.	PMID[26420067]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	Root Bark	n.a.	n.a.	PMID[26982999]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27400088]
NPO5986	Ziziphus jujuba	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27617953]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	stem	n.a.	PMID[27914541]
NPO5986	Ziziphus jujuba	Species	Rhamnaceae	Eukaryota	Roots	n.a.	n.a.	PMID[28257196]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	Flower Buds	n.a.	n.a.	PMID[28345906]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32129622]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	Rhizomes	n.a.	n.a.	PMID[8482946]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	fruits	n.a.	n.a.	PMID[9090870]
NPO12320	Adonis amurensis	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5986	Ziziphus jujuba	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16741	Codonopsis pilosula	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12320	Adonis amurensis	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5986	Ziziphus jujuba	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16741	Codonopsis pilosula	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12320	Adonis amurensis	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16741	Codonopsis pilosula	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5986	Ziziphus jujuba	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16741	Codonopsis pilosula	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO5986	Ziziphus jujuba	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26741	Anemarrhena asphodeloides	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16741	Codonopsis pilosula	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12320	Adonis amurensis	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29141	Panax ginseng	Species	Araliaceae	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 NPC88481 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	347
0.1-0.2	1431
0.2-0.3	3088
0.3-0.4	9485
0.4-0.5	19495
0.5-0.6	6926
0.6-0.7	1648
0.7-0.8	88
0.8-0.85	47
0.85-0.9	97
0.9-0.95	45
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 NPC88481 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	225
0.1-0.2	544
0.2-0.3	697
0.3-0.4	1811
0.4-0.5	3525
0.5-0.6	1934
0.6-0.7	401
0.7-0.8	13
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