NPASS Compound

Structure

NPC98759 OpenBabel06302215142D 32 36 0 0 1 0 0 0 0 0999 V2000 0.1546 1.1745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8426 0.4865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7415 0.8588 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6852 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6852 -0.9730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8426 -1.4595 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6852 -1.9459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8426 -2.4324 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.9189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8426 -2.4324 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8426 -4.3784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -4.8649 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8426 -1.4595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6852 -0.9730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5279 -1.4595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5279 -2.4324 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3705 -2.9189 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3705 -1.9459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2131 -2.4324 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0557 -2.9189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0557 -3.8919 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2131 -4.3784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6996 -5.2210 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7266 -5.2210 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3705 -3.8919 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5279 -4.3784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6852 -3.8919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6852 -2.9189 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8426 -3.4054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8983 -4.3784 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.9730 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 2 1 0 0 0 0 2 32 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 31 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 9 10 1 0 0 0 0 10 28 1 0 0 0 0 10 11 1 6 0 0 0 10 13 1 0 0 0 0 11 12 1 0 0 0 0 13 14 2 0 0 0 0 13 31 1 0 0 0 0 14 15 1 0 0 0 0 16 15 1 6 0 0 0 16 17 1 0 0 0 0 16 28 1 0 0 0 0 17 25 1 0 0 0 0 17 18 1 1 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 21 30 1 6 0 0 0 22 23 1 0 0 0 0 22 24 1 0 0 0 0 22 25 1 0 0 0 0 25 26 1 1 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 1 0 0 0 31 32 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	442.38
Volume:	499.598
LogP:	6.335
LogD:	5.03
LogS:	-6.002
# Rotatable Bonds:	1
TPSA:	40.46
# H-Bond Aceptor:	2
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.424
Synthetic Accessibility Score:	4.749
Fsp3:	0.933
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.95
MDCK Permeability:	9.890924047795124e-06
Pgp-inhibitor:	0.003
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.821
30% Bioavailability (F30%):	0.769

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.079
Plasma Protein Binding (PPB):	98.26282501220703%
Volume Distribution (VD):	1.185
Pgp-substrate:	1.7475436925888062%

ADMET: Metabolism

CYP1A2-inhibitor:	0.038
CYP1A2-substrate:	0.316
CYP2C19-inhibitor:	0.073
CYP2C19-substrate:	0.89
CYP2C9-inhibitor:	0.199
CYP2C9-substrate:	0.548
CYP2D6-inhibitor:	0.041
CYP2D6-substrate:	0.784
CYP3A4-inhibitor:	0.377
CYP3A4-substrate:	0.294

ADMET: Excretion

Clearance (CL):	4.854
Half-life (T1/2):	0.099

ADMET: Toxicity

hERG Blockers:	0.068
Human Hepatotoxicity (H-HT):	0.147
Drug-inuced Liver Injury (DILI):	0.012
AMES Toxicity:	0.006
Rat Oral Acute Toxicity:	0.08
Maximum Recommended Daily Dose:	0.935
Skin Sensitization:	0.824
Carcinogencity:	0.007
Eye Corrosion:	0.081
Eye Irritation:	0.791
Respiratory Toxicity:	0.937

Download Data

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

Natural Product: NPC98759

Natural Product ID:	NPC98759
*Common Name:**	VKFYBVXBUHHZMW-CWLHSXRESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VKFYBVXBUHHZMW-CWLHSXRESA-N
Standard InCHI:	InChI=1S/C30H50O2/c1-25(2)14-15-27(5)16-17-30(19-31)20(21(27)18-25)8-9-23-28(6)12-11-24(32)26(3,4)22(28)10-13-29(23,30)7/h8,21-24,31-32H,9-19H2,1-7H3/t21-,22-,23-,24+,27+,28-,29+,30-/m0/s1
SMILES:	CC1(C)CC[C@]2(C)CC[C@]3(CO)C(=CC[C@H]4[C@@]5(C)CC[C@H](C(C)(C)[C@@H]5CC[C@@]34C)O)[C@@H]2C1
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]
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]
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]

☑ 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 NPC98759 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	206
0.1-0.2	1733
0.2-0.3	7057
0.3-0.4	16582
0.4-0.5	7125
0.5-0.6	4848
0.6-0.7	3636
0.7-0.8	1091
0.8-0.85	269
0.85-0.9	109
0.9-0.95	13
0.95-1	28

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 NPC98759 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	192
0.1-0.2	1988
0.2-0.3	4189
0.3-0.4	1958
0.4-0.5	453
0.5-0.6	204
0.6-0.7	146
0.7-0.8	17
0.8-0.85	2
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