NPASS Compound

Structure

NPC7617 OpenBabel06302215392D 28 30 0 0 1 0 0 0 0 0999 V2000 -3.5850 -0.6688 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5922 -0.7882 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0538 0.0545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0593 0.1591 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3575 -0.5533 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6236 -0.3600 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1106 -1.2335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4304 -1.9665 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4769 -1.5461 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3276 -2.0718 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2690 -1.7345 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8826 -0.9512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8714 -1.1002 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6703 -0.2631 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5633 0.8262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4339 0.9010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1294 1.7272 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1266 1.6525 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6900 2.4787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6872 2.4040 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2561 3.3797 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8194 4.2059 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2589 3.4544 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2355 -0.0746 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2599 0.9251 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4064 1.4461 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1379 1.4038 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 11 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 9 1 0 0 0 0 5 6 1 0 0 0 0 5 25 1 1 0 0 0 6 7 1 6 0 0 0 6 15 1 0 0 0 0 7 8 1 0 0 0 0 9 8 1 6 0 0 0 9 10 1 0 0 0 0 9 12 1 0 0 0 0 10 11 2 0 0 0 0 12 13 2 0 0 0 0 12 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 1 0 0 0 15 17 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 22 23 2 0 0 0 0 22 24 1 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 26 28 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	386.17
Volume:	397.685
LogP:	1.932
LogD:	0.722
LogS:	-3.449
# Rotatable Bonds:	5
TPSA:	89.9
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.452
Synthetic Accessibility Score:	5.562
Fsp3:	0.5
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:	-5.286
MDCK Permeability:	2.0261168174329214e-05
Pgp-inhibitor:	0.016
Pgp-substrate:	0.167
Human Intestinal Absorption (HIA):	0.249
20% Bioavailability (F20%):	0.773
30% Bioavailability (F30%):	0.946

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.76
Plasma Protein Binding (PPB):	69.71341705322266%
Volume Distribution (VD):	0.255
Pgp-substrate:	21.593887329101562%

ADMET: Metabolism

CYP1A2-inhibitor:	0.023
CYP1A2-substrate:	0.556
CYP2C19-inhibitor:	0.101
CYP2C19-substrate:	0.2
CYP2C9-inhibitor:	0.105
CYP2C9-substrate:	0.422
CYP2D6-inhibitor:	0.388
CYP2D6-substrate:	0.163
CYP3A4-inhibitor:	0.574
CYP3A4-substrate:	0.26

ADMET: Excretion

Clearance (CL):	1.725
Half-life (T1/2):	0.756

ADMET: Toxicity

hERG Blockers:	0.066
Human Hepatotoxicity (H-HT):	0.667
Drug-inuced Liver Injury (DILI):	0.212
AMES Toxicity:	0.014
Rat Oral Acute Toxicity:	0.8
Maximum Recommended Daily Dose:	0.817
Skin Sensitization:	0.727
Carcinogencity:	0.883
Eye Corrosion:	0.004
Eye Irritation:	0.042
Respiratory Toxicity:	0.845

Download Data

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

Natural Product: NPC7617

Natural Product ID:	NPC7617
*Common Name:**	DMDYDVXEMCPQPC-MPVZDDSSSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DMDYDVXEMCPQPC-MPVZDDSSSA-N
Standard InCHI:	InChI=1S/C22H26O6/c1-14-7-11-21-12-9-17(22(21,13-8-14)27-16(3)23)20(4,28-19(21)26)10-5-6-15(2)18(24)25/h5-8,10-11,17H,9,12-13H2,1-4H3,(H,24,25)/b10-5+,15-6+/t17-,20+,21+,22-/m0/s1
SMILES:	CC1=CC[C@@]2([C@H]3CC[C@]2(C=C1)C(=O)O[C@]3(C)/C=C/C=C(C)/C(=O)O)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11783999
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0001538] Diterpene lactones

*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
NPO22309	Gastrodia elata	Species	Orchidaceae	Eukaryota	n.a.	tuber	n.a.	PMID[15180301]
NPO22309	Gastrodia elata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17381154]
NPO385	Bipolaris oryzae	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23668986]
NPO22309	Gastrodia elata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25843525]
NPO22309	Gastrodia elata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20140	Aloe perryi	Species	Xanthorrhoeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22239	Hibiscus vitifolius	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5178	Pelophylax nigromaculatus	Species	Ranidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22309	Gastrodia elata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22239	Hibiscus vitifolius	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20140	Aloe perryi	Species	Xanthorrhoeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22309	Gastrodia elata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO22309	Gastrodia elata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO22563	Sclerocarya birrea	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22239	Hibiscus vitifolius	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22700	Dacrydium comosum	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21914	Turnera angustifolia	Species	Passifloraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO385	Bipolaris oryzae	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20328	Plumeria acutifolia	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22309	Gastrodia elata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21090	Chrysanthemum ornatum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20772	Pedalium murex	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5178	Pelophylax nigromaculatus	Species	Ranidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20262	Delia paludosa	Species	Anthomyiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20140	Aloe perryi	Species	Xanthorrhoeaceae	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 NPC7617 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	183
0.1-0.2	1001
0.2-0.3	4000
0.3-0.4	9143
0.4-0.5	14465
0.5-0.6	7718
0.6-0.7	5275
0.7-0.8	887
0.8-0.85	13
0.85-0.9	4
0.9-0.95	4
0.95-1	4

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 NPC7617 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	163
0.1-0.2	1225
0.2-0.3	3508
0.3-0.4	2786
0.4-0.5	942
0.5-0.6	284
0.6-0.7	222
0.7-0.8	20
0.8-0.85	0
0.85-0.9	0
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