NPASS Compound

Structure

NPC59462 OpenBabel06302216212D 33 37 0 0 1 0 0 0 0 0999 V2000 -0.1082 -1.6693 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8475 -1.4659 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8472 -0.4888 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6930 0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6927 0.9780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 0.9775 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0006 1.9775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8475 1.4663 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8478 2.4444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6950 2.9332 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5420 2.4440 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3886 2.9328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3889 3.9328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2547 3.4328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2350 2.4435 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2347 1.4654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3881 0.9765 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5417 1.4658 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5414 0.4877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6945 0.9770 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6942 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8470 -0.4893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0003 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1013 2.9431 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5015 -2.1919 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1999 -3.1212 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2442 -3.3247 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0575 -4.2540 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1459 -5.2097 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8719 -4.5557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0132 -4.4575 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4572 -1.9884 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 26 1 0 0 0 0 3 2 1 6 0 0 0 3 4 1 0 0 0 0 3 23 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 23 1 0 0 0 0 6 7 1 1 0 0 0 6 8 1 0 0 0 0 8 9 1 1 0 0 0 8 20 1 0 0 0 0 9 10 1 0 0 0 0 11 10 1 6 0 0 0 11 12 1 0 0 0 0 11 18 1 0 0 0 0 12 13 1 0 0 0 0 12 14 1 0 0 0 0 12 15 1 0 0 0 0 15 16 1 0 0 0 0 15 25 1 6 0 0 0 16 17 1 0 0 0 0 18 17 1 1 0 0 0 18 20 1 0 0 0 0 18 19 1 0 0 0 0 20 19 1 6 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 6 0 0 0 26 27 1 0 0 0 0 26 33 1 6 0 0 0 27 28 2 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 29 31 1 0 0 0 0 29 32 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	458.38
Volume:	508.388
LogP:	5.168
LogD:	4.353
LogS:	-4.645
# Rotatable Bonds:	4
TPSA:	60.69
# H-Bond Aceptor:	3
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.445
Synthetic Accessibility Score:	5.753
Fsp3:	0.933
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.91
MDCK Permeability:	1.768392394296825e-05
Pgp-inhibitor:	0.048
Pgp-substrate:	0.012
Human Intestinal Absorption (HIA):	0.013
20% Bioavailability (F20%):	0.198
30% Bioavailability (F30%):	0.98

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.28
Plasma Protein Binding (PPB):	90.47969818115234%
Volume Distribution (VD):	1.087
Pgp-substrate:	1.2557823657989502%

ADMET: Metabolism

CYP1A2-inhibitor:	0.012
CYP1A2-substrate:	0.307
CYP2C19-inhibitor:	0.046
CYP2C19-substrate:	0.888
CYP2C9-inhibitor:	0.187
CYP2C9-substrate:	0.281
CYP2D6-inhibitor:	0.023
CYP2D6-substrate:	0.302
CYP3A4-inhibitor:	0.883
CYP3A4-substrate:	0.502

ADMET: Excretion

Clearance (CL):	6.019
Half-life (T1/2):	0.157

ADMET: Toxicity

hERG Blockers:	0.061
Human Hepatotoxicity (H-HT):	0.364
Drug-inuced Liver Injury (DILI):	0.022
AMES Toxicity:	0.002
Rat Oral Acute Toxicity:	0.952
Maximum Recommended Daily Dose:	0.98
Skin Sensitization:	0.854
Carcinogencity:	0.137
Eye Corrosion:	0.004
Eye Irritation:	0.031
Respiratory Toxicity:	0.972

Download Data

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

Natural Product: NPC59462

Natural Product ID:	NPC59462
*Common Name:**	JQQHNCBIPFJTGF-YDLGJMQMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JQQHNCBIPFJTGF-YDLGJMQMSA-N
Standard InCHI:	InChI=1S/C30H50O3/c1-19(21(31)11-13-25(2,3)33)20-10-14-28(7)23-9-8-22-26(4,5)24(32)12-15-29(22)18-30(23,29)17-16-27(20,28)6/h11,13,19-24,31-33H,8-10,12,14-18H2,1-7H3/b13-11+/t19-,20+,21+,22-,23-,24-,27+,28-,29+,30-/m0/s1
SMILES:	C[C@@H]([C@H]1CC[C@@]2(C)[C@@H]3CC[C@H]4C(C)(C)[C@H](CC[C@]54C[C@@]35CC[C@]12C)O)[C@@H](/C=C/C(C)(C)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11453918
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002321] Cycloartanols 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
NPO13608	Plumbago zeylanica	Species	Plumbaginaceae	Eukaryota	n.a.	root	n.a.	PMID[16078700]
NPO13608	Plumbago zeylanica	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23848163]
NPO16020	Corydalis taliensis	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10985	Scutellaria discolor	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13608	Plumbago zeylanica	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16315	Xylopia columbiana	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16020	Corydalis taliensis	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13608	Plumbago zeylanica	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16315	Xylopia columbiana	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10985	Scutellaria discolor	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13608	Plumbago zeylanica	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16468	Brya ebenus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2791	Macfadyena cynanchoides	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12279	Roldana sessilifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9713	Philotheca myoporoides	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4831	Meridiastra calcar	Species	Asterinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15197	Amberboa ramosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16020	Corydalis taliensis	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14451	Rabdosia macrocalyx	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5233	Acer pycnanthum	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16315	Xylopia columbiana	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10985	Scutellaria discolor	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14132	Pseudonocardia compacta	Species	Pseudonocardiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO14643	Eriocephalus scariosus	Species	Asteraceae	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 NPC59462 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	171
0.1-0.2	1518
0.2-0.3	6873
0.3-0.4	15987
0.4-0.5	7249
0.5-0.6	5887
0.6-0.7	3769
0.7-0.8	1019
0.8-0.85	157
0.85-0.9	52
0.9-0.95	13
0.95-1	2

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 NPC59462 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	170
0.1-0.2	1709
0.2-0.3	4418
0.3-0.4	2026
0.4-0.5	410
0.5-0.6	185
0.6-0.7	181
0.7-0.8	50
0.8-0.85	0
0.85-0.9	1
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