NPASS Compound

Structure

NPC50021 OpenBabel06302215412D 51 58 0 0 1 0 0 0 0 0999 V2000 -1.5265 0.8813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5088 0.8813 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 1.7626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0176 1.7626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5265 0.8813 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.1031 1.6749 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7886 2.6428 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0360 1.3718 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.0360 0.3908 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.8857 -0.1004 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7364 1.3711 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.5871 1.8616 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.4372 1.3702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2880 1.8607 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2886 2.8427 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1390 3.3327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1393 4.3142 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.2892 4.8057 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4387 4.3157 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.4384 3.3342 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.5614 3.8412 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5877 2.8437 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.7381 3.3348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8874 2.8443 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8868 1.8623 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.0097 2.3694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5890 4.8069 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2863 5.7406 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3263 5.9452 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.0236 6.8788 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.6808 7.6078 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.6407 7.4032 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.2979 8.1322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9435 6.4696 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3780 8.5415 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0637 7.0835 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6692 5.2162 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.9895 4.8046 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.7186 4.1475 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 10.6522 4.4504 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 11.3813 3.7933 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 11.1768 2.8333 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 10.2432 2.5304 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 10.0387 1.5705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5141 3.1875 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 11.9059 2.1763 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 12.3149 4.0962 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.8567 5.4103 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1031 0.0877 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0176 -0.0000 0.0000 O 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 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 51 1 0 0 0 0 3 4 1 0 0 0 0 5 4 1 6 0 0 0 5 49 1 0 0 0 0 5 6 1 0 0 0 0 5 50 1 0 0 0 0 6 7 1 1 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 8 25 1 0 0 0 0 9 10 1 0 0 0 0 9 49 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 25 1 0 0 0 0 12 13 1 0 0 0 0 12 22 1 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 15 20 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 38 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 19 27 1 0 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 28 34 1 0 0 0 0 29 30 1 0 0 0 0 29 37 1 0 0 0 0 30 31 1 0 0 0 0 30 36 1 0 0 0 0 31 32 1 0 0 0 0 31 35 1 0 0 0 0 32 33 1 1 0 0 0 32 34 1 0 0 0 0 39 38 1 1 0 0 0 39 40 1 0 0 0 0 39 45 1 0 0 0 0 40 41 1 0 0 0 0 40 48 1 6 0 0 0 41 42 1 0 0 0 0 41 47 1 6 0 0 0 42 43 1 0 0 0 0 42 46 1 1 0 0 0 43 44 1 6 0 0 0 43 45 1 0 0 0 0 50 51 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	722.42
Volume:	717.494
LogP:	3.689
LogD:	3.241
LogS:	-4.456
# Rotatable Bonds:	4
TPSA:	176.76
# H-Bond Aceptor:	12
# H-Bond Donor:	6
# Rings:	8
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.234
Synthetic Accessibility Score:	6.354
Fsp3:	0.949
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:	-5.858
MDCK Permeability:	8.321813947986811e-05
Pgp-inhibitor:	0.404
Pgp-substrate:	0.679
Human Intestinal Absorption (HIA):	0.189
20% Bioavailability (F20%):	0.063
30% Bioavailability (F30%):	0.913

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.003
Plasma Protein Binding (PPB):	75.14254760742188%
Volume Distribution (VD):	0.398
Pgp-substrate:	7.07318639755249%

ADMET: Metabolism

CYP1A2-inhibitor:	0.004
CYP1A2-substrate:	0.383
CYP2C19-inhibitor:	0.009
CYP2C19-substrate:	0.392
CYP2C9-inhibitor:	0.007
CYP2C9-substrate:	0.008
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.069
CYP3A4-inhibitor:	0.096
CYP3A4-substrate:	0.09

ADMET: Excretion

Clearance (CL):	2.153
Half-life (T1/2):	0.608

ADMET: Toxicity

hERG Blockers:	0.961
Human Hepatotoxicity (H-HT):	0.185
Drug-inuced Liver Injury (DILI):	0.778
AMES Toxicity:	0.371
Rat Oral Acute Toxicity:	0.065
Maximum Recommended Daily Dose:	0.259
Skin Sensitization:	0.941
Carcinogencity:	0.281
Eye Corrosion:	0.003
Eye Irritation:	0.011
Respiratory Toxicity:	0.971

Download Data

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

Natural Product: NPC50021

Natural Product ID:	NPC50021
*Common Name:**	RMIQIULKBBCLIL-KJXSMTROSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RMIQIULKBBCLIL-KJXSMTROSA-N
Standard InCHI:	InChI=1S/C39H62O12/c1-17-9-12-39(46-16-17)18(2)28-26(51-39)15-25-23-8-7-21-13-22(49-35-33(44)31(42)29(40)19(3)47-35)14-27(38(21,6)24(23)10-11-37(25,28)5)50-36-34(45)32(43)30(41)20(4)48-36/h7,17-20,22-36,40-45H,8-16H2,1-6H3/t17-,18-,19-,20+,22+,23+,24-,25-,26-,27+,28-,29-,30-,31+,32-,33+,34+,35-,36-,37-,38-,39+/m0/s1
SMILES:	C[C@H]1CC[C@@]2([C@@H](C)[C@H]3[C@H](C[C@H]4[C@@H]5CC=C6C[C@H](C[C@H]([C@]6(C)[C@H]5CC[C@]34C)O[C@H]3[C@@H]([C@H]([C@H]([C@@H](C)O3)O)O)O)O[C@H]3[C@@H]([C@@H]([C@H]([C@H](C)O3)O)O)O)O2)OC1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	21630160
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001013] Steroidal glycosides [CHEMONTID:0002364] Steroidal saponins

*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
NPO9261	Ophiopogon japonicus	Species	Asparagaceae	Eukaryota	roots	n.a.	n.a.	PMID[20346658]
NPO9261	Ophiopogon japonicus	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23439553]
NPO9261	Ophiopogon japonicus	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO9261	Ophiopogon japonicus	Species	Asparagaceae	Eukaryota	n.a.	tuber	n.a.	Database[Article]
NPO9261	Ophiopogon japonicus	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5275	Liriope muscari	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9261	Ophiopogon japonicus	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9261	Ophiopogon japonicus	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9261	Ophiopogon japonicus	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO5275	Liriope muscari	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9261	Ophiopogon japonicus	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5275	Liriope muscari	Species	Asparagaceae	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 NPC50021 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	307
0.1-0.2	2116
0.2-0.3	6998
0.3-0.4	13964
0.4-0.5	8600
0.5-0.6	5431
0.6-0.7	3022
0.7-0.8	1391
0.8-0.85	520
0.85-0.9	192
0.9-0.95	76
0.95-1	80

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 NPC50021 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	245
0.1-0.2	2279
0.2-0.3	4384
0.3-0.4	1474
0.4-0.5	406
0.5-0.6	244
0.6-0.7	90
0.7-0.8	14
0.8-0.85	9
0.85-0.9	5
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