NPASS Compound

Structure

NPC49846 OpenBabel06302216172D 32 35 0 0 1 0 0 0 0 0999 V2000 -1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1962 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6962 -1.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 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 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 14 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 5 4 1 1 0 0 0 5 6 1 0 0 0 0 5 12 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 6 9 1 0 0 0 0 9 10 1 0 0 0 0 9 32 1 1 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 1 0 0 0 12 14 1 0 0 0 0 14 15 1 1 0 0 0 15 16 1 0 0 0 0 17 16 1 6 0 0 0 17 18 1 0 0 0 0 17 28 1 0 0 0 0 18 19 1 0 0 0 0 18 31 1 6 0 0 0 19 20 1 0 0 0 0 21 20 1 6 0 0 0 21 22 1 0 0 0 0 21 28 1 0 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 0 0 0 0 25 30 1 6 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	446.38
Volume:	499.648
LogP:	5.328
LogD:	5.057
LogS:	-4.692
# Rotatable Bonds:	3
TPSA:	60.69
# H-Bond Aceptor:	3
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.458
Synthetic Accessibility Score:	4.827
Fsp3:	0.931
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:	-4.768
MDCK Permeability:	1.5845340385567397e-05
Pgp-inhibitor:	0.968
Pgp-substrate:	0.326
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.985
30% Bioavailability (F30%):	0.95

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.191
Plasma Protein Binding (PPB):	84.86377716064453%
Volume Distribution (VD):	0.903
Pgp-substrate:	7.775319576263428%

ADMET: Metabolism

CYP1A2-inhibitor:	0.023
CYP1A2-substrate:	0.146
CYP2C19-inhibitor:	0.031
CYP2C19-substrate:	0.806
CYP2C9-inhibitor:	0.139
CYP2C9-substrate:	0.274
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.657
CYP3A4-inhibitor:	0.1
CYP3A4-substrate:	0.241

ADMET: Excretion

Clearance (CL):	9.219
Half-life (T1/2):	0.063

ADMET: Toxicity

hERG Blockers:	0.031
Human Hepatotoxicity (H-HT):	0.211
Drug-inuced Liver Injury (DILI):	0.014
AMES Toxicity:	0.005
Rat Oral Acute Toxicity:	0.89
Maximum Recommended Daily Dose:	0.994
Skin Sensitization:	0.331
Carcinogencity:	0.02
Eye Corrosion:	0.08
Eye Irritation:	0.068
Respiratory Toxicity:	0.964

Download Data

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

Natural Product: NPC49846

Natural Product ID:	NPC49846
*Common Name:**	TVYHTITYAHKAKA-AOCQSIBXSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	TVYHTITYAHKAKA-AOCQSIBXSA-N
Standard InCHI:	InChI=1S/C29H50O3/c1-18-8-12-22-26(2,3)24(31)14-16-28(22,6)19(18)9-10-20-21(30)11-13-23-27(4,5)25(32)15-17-29(20,23)7/h19-25,30-32H,1,8-17H2,2-7H3/t19-,20-,21-,22-,23-,24-,25-,28+,29+/m0/s1
SMILES:	C=C1CC[C@H]2C(C)(C)[C@H](CC[C@]2(C)[C@H]1CC[C@H]1[C@H](CC[C@H]2C(C)(C)[C@H](CC[C@]12C)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	46894237
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000129] Alcohols and polyols [CHEMONTID:0001292] Cyclic alcohols 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
NPO29428	Dalbergia cochinchinensis	Species	Fabaceae	Eukaryota	n.a.	seed	n.a.	DOI[10.1016/S0031-9422(98)00552-4]
NPO29428	Dalbergia cochinchinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12932142]
NPO24855	Callicarpa americana	Species	Lamiaceae	Eukaryota	fruiting branches	n.a.	n.a.	PMID[17279798]
NPO29428	Dalbergia cochinchinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29460	Petiveria alliacea	Species	Petiveriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27912	Cocculus laurifolius	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29460	Petiveria alliacea	Species	Petiveriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27912	Cocculus laurifolius	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29428	Dalbergia cochinchinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29277	Lycopodium obscurum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29428	Dalbergia cochinchinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27912	Cocculus laurifolius	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29460	Petiveria alliacea	Species	Petiveriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29277	Lycopodium obscurum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28418	Grateloupia filicina	Species	Halymeniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27912	Cocculus laurifolius	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29521	Genista purgans	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29247	Wahlenbergia marginata	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27937	Centaurea iberica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18357	Euphorbia sanctae-catharinae	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24855	Callicarpa americana	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27125	Hovea linearis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26339	Dillenia philippinensis	Species	Dilleniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24832	Eriocaulon ligulatum	Species	Eriocaulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24225	Alexandrium peruvianum	Species	Gonyaulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25798	Gunnera perpensa	Species	Gunneraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26498	Vernonia cumingiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22646	Malouetia tamaquarina	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28055	Perymenium berlandieri	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29087	Ligularia brachyphylla	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27361	Hylobius abietis	Species	Curculionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29261	Bryothamnion triquetrum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO21044	Sphaerellopsis filum	Species	Leptosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26989	Delphinium geyeri	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24978	Psila boliviensis	Species	Psilidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26662	Chrysanthemum foeniculaceum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29522	Cuscuta salina	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29428	Dalbergia cochinchinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24542	Doris obsoleta	Species	Dorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26775	Shorea wangtianshuea	Species	Dipterocarpaceae	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 NPC49846 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	220
0.1-0.2	2309
0.2-0.3	10365
0.3-0.4	15603
0.4-0.5	5510
0.5-0.6	4930
0.6-0.7	2718
0.7-0.8	846
0.8-0.85	125
0.85-0.9	59
0.9-0.95	12
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 NPC49846 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	189
0.1-0.2	2729
0.2-0.3	4046
0.3-0.4	1572
0.4-0.5	302
0.5-0.6	219
0.6-0.7	82
0.7-0.8	9
0.8-0.85	1
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