NPASS Compound

Structure

NPC50302 OpenBabel06302215592D 34 38 0 0 1 0 0 0 0 0999 V2000 -0.1548 -1.1762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8438 -0.4872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7440 -0.8601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6876 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6876 0.9744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8438 1.4615 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8438 2.4359 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.9231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8438 2.4359 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8438 4.3846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8438 1.4615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6876 0.9744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5315 1.4615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5315 2.4359 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3753 2.9231 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3753 1.9487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2191 2.4359 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0629 2.9231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0629 3.8974 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2191 4.3846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7063 5.2284 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7319 5.2284 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3753 3.8974 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5315 4.3846 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6876 3.8974 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6876 2.9231 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8438 3.4103 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5315 5.3590 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9067 4.3846 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.9744 0.0000 C 0 0 2 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 -1.6876 1.9487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6876 2.9231 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5315 1.4615 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 31 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 30 1 0 0 0 0 6 7 1 0 0 0 0 6 32 1 1 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 26 1 0 0 0 0 9 10 1 6 0 0 0 9 11 1 0 0 0 0 11 12 2 0 0 0 0 11 30 1 0 0 0 0 12 13 1 0 0 0 0 14 13 1 1 0 0 0 14 15 1 0 0 0 0 14 26 1 0 0 0 0 15 23 1 0 0 0 0 15 16 1 1 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 19 29 1 6 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 23 20 1 1 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 24 28 1 6 0 0 0 25 26 1 0 0 0 0 26 27 1 1 0 0 0 30 31 1 6 0 0 0 32 33 2 0 0 0 0 32 34 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	364.12
Volume:	348.718
LogP:	1.532
LogD:	1.48
LogS:	-3.704
# Rotatable Bonds:	7
TPSA:	111.52
# H-Bond Aceptor:	8
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.556
Synthetic Accessibility Score:	4.693
Fsp3:	0.444
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.117
MDCK Permeability:	2.840943488990888e-05
Pgp-inhibitor:	0.034
Pgp-substrate:	0.211
Human Intestinal Absorption (HIA):	0.085
20% Bioavailability (F20%):	0.063
30% Bioavailability (F30%):	0.962

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.9
Plasma Protein Binding (PPB):	55.77674865722656%
Volume Distribution (VD):	0.95
Pgp-substrate:	24.459516525268555%

ADMET: Metabolism

CYP1A2-inhibitor:	0.513
CYP1A2-substrate:	0.2
CYP2C19-inhibitor:	0.138
CYP2C19-substrate:	0.418
CYP2C9-inhibitor:	0.209
CYP2C9-substrate:	0.049
CYP2D6-inhibitor:	0.016
CYP2D6-substrate:	0.163
CYP3A4-inhibitor:	0.197
CYP3A4-substrate:	0.456

ADMET: Excretion

Clearance (CL):	6.329
Half-life (T1/2):	0.629

ADMET: Toxicity

hERG Blockers:	0.045
Human Hepatotoxicity (H-HT):	0.079
Drug-inuced Liver Injury (DILI):	0.929
AMES Toxicity:	0.235
Rat Oral Acute Toxicity:	0.019
Maximum Recommended Daily Dose:	0.015
Skin Sensitization:	0.729
Carcinogencity:	0.374
Eye Corrosion:	0.02
Eye Irritation:	0.802
Respiratory Toxicity:	0.049

Download Data

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

Natural Product: NPC50302

Natural Product ID:	NPC50302
*Common Name:**	KLHSKTMVSOWVLD-SBAVZYBFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KLHSKTMVSOWVLD-SBAVZYBFSA-N
Standard InCHI:	InChI=1S/C30H48O4/c1-25(2)12-14-30(24(33)34)15-13-28(6)18(19(30)16-25)8-9-21-27(5)11-10-22(32)26(3,4)23(27)20(31)17-29(21,28)7/h8,19-23,31-32H,9-17H2,1-7H3,(H,33,34)/t19-,20-,21+,22+,23-,27+,28+,29+,30-/m0/s1
SMILES:	CC1(C)CC[C@@]2(CC[C@]3(C)C(=CC[C@@H]4[C@@]5(C)CC[C@H](C(C)(C)[C@@H]5[C@H](C[C@@]34C)O)O)[C@@H]2C1)C(=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO17030	Calvatia lilacina	Species	Lycoperdaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO2591	Io fluvialis	Species	Pleuroceridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9524	Kalanchoe blossfeldiana	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13182	Achillea wilhelmsii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16377	Juniperus ashei	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18768	Haliclona tubifera	Species	Chalinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6746	Blighia welwitschii	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17373.1	Cunninghamia lanceolata var. konishii	Varieties	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17707	Dioscorea villosa	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3446	Acanthaster planci	Species	Acanthasteridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18031	Russula vesca	Species	Russulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16254	Backhousia angustifolia	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15966	Sassafras officinalis	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23695	Setosphaeria turcica	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17030	Calvatia lilacina	Species	Lycoperdaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3990	Acacia salicina	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10438	Tanacetum nubigenum	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 NPC50302 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	203
0.1-0.2	1325
0.2-0.3	4873
0.3-0.4	14419
0.4-0.5	8727
0.5-0.6	5398
0.6-0.7	4851
0.7-0.8	2154
0.8-0.85	358
0.85-0.9	128
0.9-0.95	144
0.95-1	117

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 NPC50302 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	182
0.1-0.2	1666
0.2-0.3	3830
0.3-0.4	2330
0.4-0.5	676
0.5-0.6	210
0.6-0.7	169
0.7-0.8	79
0.8-0.85	3
0.85-0.9	2
0.9-0.95	2
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