NPASS Compound

Structure

NPC224581 OpenBabel06302216202D 35 39 0 0 1 0 0 0 0 0999 V2000 -1.6811 -1.2743 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3863 -0.3187 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.0884 -0.4790 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5782 0.0489 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3659 0.7370 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6639 0.8972 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8864 1.8722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1741 0.3694 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4721 0.5296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0177 0.0018 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1945 -0.6863 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7823 -1.4954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1945 -2.3044 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8966 -2.1441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2090 -1.4954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8966 -0.8466 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7565 -1.9954 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7565 -0.9954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7511 -2.0999 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3388 -1.2909 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9321 -0.3773 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5199 0.4317 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.1132 1.3452 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.1186 1.4498 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5308 0.6407 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4637 0.7453 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8704 1.6588 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9376 -0.2728 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7119 2.3633 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7009 2.1542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5144 0.3272 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1633 -2.9089 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9308 1.5774 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1534 2.5523 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0247 1.2827 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 8 1 0 0 0 0 2 16 1 0 0 0 0 2 3 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 6 8 1 0 0 0 0 6 33 1 0 0 0 0 8 9 1 1 0 0 0 9 10 1 0 0 0 0 11 10 1 1 0 0 0 11 18 1 0 0 0 0 11 12 1 0 0 0 0 11 16 1 0 0 0 0 13 12 1 1 0 0 0 13 14 1 0 0 0 0 13 17 1 0 0 0 0 14 15 1 0 0 0 0 16 15 1 1 0 0 0 17 18 1 0 0 0 0 17 19 1 0 0 0 0 17 32 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 31 1 1 0 0 0 23 24 1 0 0 0 0 23 30 1 6 0 0 0 24 25 1 0 0 0 0 24 29 1 1 0 0 0 25 26 1 6 0 0 0 25 28 1 0 0 0 0 26 27 1 0 0 0 0 33 34 2 0 0 0 0 33 35 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	498.28
Volume:	491.945
LogP:	-0.563
LogD:	1.041
LogS:	-2.885
# Rotatable Bonds:	5
TPSA:	156.91
# H-Bond Aceptor:	9
# H-Bond Donor:	6
# Rings:	5
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.326
Synthetic Accessibility Score:	6.17
Fsp3:	0.962
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.161
MDCK Permeability:	2.5459950848016888e-05
Pgp-inhibitor:	0.545
Pgp-substrate:	0.938
Human Intestinal Absorption (HIA):	0.893
20% Bioavailability (F20%):	0.731
30% Bioavailability (F30%):	0.976

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.126
Plasma Protein Binding (PPB):	67.49219512939453%
Volume Distribution (VD):	0.384
Pgp-substrate:	18.13603401184082%

ADMET: Metabolism

CYP1A2-inhibitor:	0.005
CYP1A2-substrate:	0.937
CYP2C19-inhibitor:	0.004
CYP2C19-substrate:	0.368
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.042
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.081
CYP3A4-inhibitor:	0.277
CYP3A4-substrate:	0.015

ADMET: Excretion

Clearance (CL):	1.081
Half-life (T1/2):	0.695

ADMET: Toxicity

hERG Blockers:	0.081
Human Hepatotoxicity (H-HT):	0.659
Drug-inuced Liver Injury (DILI):	0.021
AMES Toxicity:	0.121
Rat Oral Acute Toxicity:	0.011
Maximum Recommended Daily Dose:	0.551
Skin Sensitization:	0.088
Carcinogencity:	0.224
Eye Corrosion:	0.003
Eye Irritation:	0.021
Respiratory Toxicity:	0.956

Download Data

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

Natural Product: NPC224581

Natural Product ID:	NPC224581
*Common Name:**	RDJJPCDVQOJULI-WPGYLICUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RDJJPCDVQOJULI-WPGYLICUSA-N
Standard InCHI:	InChI=1S/C26H42O9/c1-23-7-3-8-24(2,22(31)32)16(23)6-9-25-10-14(4-5-17(23)25)26(33,12-25)13-34-21-20(30)19(29)18(28)15(11-27)35-21/h14-21,27-30,33H,3-13H2,1-2H3,(H,31,32)/t14-,15-,16+,17+,18-,19+,20-,21-,23-,24-,25+,26-/m1/s1
SMILES:	C[C@@]12CCC[C@](C)([C@H]1CC[C@]13C[C@@H](CC[C@@H]23)[C@@](C1)(CO[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)C(=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101692676
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001755] Diterpene glycosides

*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
NPO5326	Knema furfuracea	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8254357]
NPO6066	Graphium sarpedon	Species	Papilionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5326	Knema furfuracea	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4903	Duroia hirsuta	Species	Rubiaceae	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 NPC224581 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	446
0.1-0.2	3513
0.2-0.3	10360
0.3-0.4	11828
0.4-0.5	6333
0.5-0.6	4830
0.6-0.7	3234
0.7-0.8	1885
0.8-0.85	229
0.85-0.9	31
0.9-0.95	7
0.95-1	1

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 NPC224581 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	470
0.1-0.2	3590
0.2-0.3	3428
0.3-0.4	902
0.4-0.5	354
0.5-0.6	249
0.6-0.7	121
0.7-0.8	33
0.8-0.85	3
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