NPASS Compound

Structure

NPC225662 OpenBabel06302216202D 36 41 0 0 1 0 0 0 0 0999 V2000 2.3394 -4.7483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2955 -4.5448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5973 -3.6150 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5535 -3.4115 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8553 -2.4817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8114 -2.2782 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.4658 -3.0044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8112 -1.3006 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.6573 -0.8111 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6570 0.1669 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9632 0.1664 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.9630 1.1664 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1156 0.6554 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.1153 1.6340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2677 2.1230 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4204 1.6335 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5733 2.1225 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5730 3.1225 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7073 2.6225 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7266 1.6330 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7268 0.6545 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5739 0.1654 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4206 0.6549 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4209 -0.3236 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2683 0.1659 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.2685 -0.8121 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1162 -1.3011 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9635 -0.8116 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.9638 -1.8116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3705 -0.7913 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3978 -0.8935 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4804 -1.4006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3978 -1.9076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1397 2.1326 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9498 -5.2711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 36 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 6 0 0 0 8 6 1 6 0 0 0 8 9 1 0 0 0 0 8 28 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 28 1 0 0 0 0 11 12 1 1 0 0 0 11 13 1 0 0 0 0 13 14 1 1 0 0 0 13 25 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 23 1 0 0 0 0 17 18 1 0 0 0 0 17 19 1 0 0 0 0 17 20 1 0 0 0 0 20 21 1 0 0 0 0 20 35 1 6 0 0 0 21 22 1 0 0 0 0 21 34 1 1 0 0 0 22 23 1 0 0 0 0 22 30 1 1 0 0 0 23 25 1 0 0 0 0 23 24 1 6 0 0 0 25 24 1 6 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 6 0 0 0 30 31 1 0 0 0 0 31 32 1 0 0 0 0 31 33 1 0 0 0 0 31 34 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	498.41
Volume:	551.719
LogP:	8.612
LogD:	5.791
LogS:	-7.092
# Rotatable Bonds:	4
TPSA:	38.69
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	6
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.4
Synthetic Accessibility Score:	5.977
Fsp3:	0.939
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:	-5.038
MDCK Permeability:	1.2931233868584968e-05
Pgp-inhibitor:	0.884
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.948
30% Bioavailability (F30%):	0.924

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.048
Plasma Protein Binding (PPB):	92.54853820800781%
Volume Distribution (VD):	1.585
Pgp-substrate:	2.8293962478637695%

ADMET: Metabolism

CYP1A2-inhibitor:	0.014
CYP1A2-substrate:	0.277
CYP2C19-inhibitor:	0.119
CYP2C19-substrate:	0.927
CYP2C9-inhibitor:	0.233
CYP2C9-substrate:	0.057
CYP2D6-inhibitor:	0.022
CYP2D6-substrate:	0.13
CYP3A4-inhibitor:	0.736
CYP3A4-substrate:	0.582

ADMET: Excretion

Clearance (CL):	8.876
Half-life (T1/2):	0.028

ADMET: Toxicity

hERG Blockers:	0.754
Human Hepatotoxicity (H-HT):	0.626
Drug-inuced Liver Injury (DILI):	0.113
AMES Toxicity:	0.003
Rat Oral Acute Toxicity:	0.619
Maximum Recommended Daily Dose:	0.03
Skin Sensitization:	0.913
Carcinogencity:	0.304
Eye Corrosion:	0.015
Eye Irritation:	0.022
Respiratory Toxicity:	0.966

Download Data

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

Natural Product: NPC225662

Natural Product ID:	NPC225662
*Common Name:**	DYIJRGIOLKMBCR-WHHLIWQDSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DYIJRGIOLKMBCR-WHHLIWQDSA-N
Standard InCHI:	InChI=1S/C33H54O3/c1-20(2)11-10-12-21(3)22-15-16-31(9)24-14-13-23-28(4,5)26(34)25-27(36-29(6,7)35-25)33(23)19-32(24,33)18-17-30(22,31)8/h11,21-27,34H,10,12-19H2,1-9H3/t21-,22-,23+,24+,25+,26+,27+,30-,31+,32+,33-/m1/s1
SMILES:	CC(=CCC[C@@H](C)[C@H]1CC[C@@]2(C)[C@@H]3CC[C@H]4C(C)(C)[C@H]([C@H]5[C@@H]([C@]64C[C@@]36CC[C@]12C)OC(C)(C)O5)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101574638
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
NPO11707	Ruta chalepensis	Species	Rutaceae	Eukaryota	roots	northern Saudi desert	n.a.	PMID[10924184]
NPO6831	Commiphora opobalsamum	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18177010]
NPO7260	Angelica genuflexa	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11707	Ruta chalepensis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO817	Dictamnus angustifolius	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO817	Dictamnus angustifolius	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7260	Angelica genuflexa	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11707	Ruta chalepensis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8297	Hydnellum caeruleum	Species	Thelephoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11707	Ruta chalepensis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4463	Cytisus canariensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9639	Prunus puddum	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25831	Siphonoglossa sessilis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO3693	Calpurnia aurea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9883	Allium giganteum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6022	Cytisus supinus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11707	Ruta chalepensis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7260	Angelica genuflexa	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8985	Gazania rigens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6831	Commiphora opobalsamum	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24891	Elmerina caryae	Species	Aporpiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5284	Ramalina hierrensis	Species	Ramalinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1586	Gorgonocephalus chilensis	Species	Gorgonocephalidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5886	Fossombronia alaskana	Species	Fossombroniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8810	Pinus austriaca	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29336	Corynandra chelidonii	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8297	Hydnellum caeruleum	Species	Thelephoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO817	Dictamnus angustifolius	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10085	Aspergillus varians	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9036	Dipteryx lacunifera	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2328	Lagochilus setulosus	Species	Lamiaceae	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 NPC225662 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	243
0.1-0.2	1871
0.2-0.3	6357
0.3-0.4	14843
0.4-0.5	8255
0.5-0.6	5058
0.6-0.7	4619
0.7-0.8	1350
0.8-0.85	89
0.85-0.9	12
0.9-0.95	0
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 NPC225662 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	211
0.1-0.2	2040
0.2-0.3	4434
0.3-0.4	1678
0.4-0.5	417
0.5-0.6	221
0.6-0.7	130
0.7-0.8	19
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