NPASS Compound

Structure

NPC266330 OpenBabel06302215282D 41 42 0 0 1 0 0 0 0 0999 V2000 5.3484 -8.1090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4529 -7.1144 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6439 -6.5267 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7484 -5.5321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9394 -4.9443 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0439 -3.9498 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2349 -3.3620 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3395 -2.3675 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5304 -1.7797 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6350 -0.7852 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8259 -0.1974 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9305 0.7971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1215 1.3849 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.2079 0.9781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6581 1.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4013 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9945 -0.1045 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4945 -0.9706 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9945 -1.8366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4945 -2.7026 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4945 -2.7026 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9945 -1.8366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9945 -1.8366 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.4945 -0.9706 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4945 -0.9706 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9945 -0.1045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9945 -0.1045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4945 0.7615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.4945 0.7615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.9945 1.6275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.9945 1.6275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.5823 0.8185 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.5334 1.1275 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -12.3424 0.5397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.5334 2.1275 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.5823 2.4365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.2733 3.3876 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4945 -2.7026 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4945 -0.9706 0.0000 O 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 1.2260 2.3794 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 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 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 41 1 1 0 0 0 14 13 1 6 0 0 0 14 15 1 0 0 0 0 14 40 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 6 0 0 0 17 40 1 0 0 0 0 18 19 1 0 0 0 0 18 39 1 1 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 23 38 1 6 0 0 0 24 25 1 0 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 0 0 0 0 29 30 1 0 0 0 0 30 31 1 0 0 0 0 31 36 1 0 0 0 0 31 32 2 0 0 0 0 32 33 1 0 0 0 0 33 34 1 1 0 0 0 33 35 1 0 0 0 0 35 36 1 0 0 0 0 36 37 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	410.17
Volume:	415.164
LogP:	6.032
LogD:	3.812
LogS:	-5.597
# Rotatable Bonds:	2
TPSA:	78.13
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.616
Synthetic Accessibility Score:	3.75
Fsp3:	0.458
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:	-4.781
MDCK Permeability:	1.807021180866286e-05
Pgp-inhibitor:	0.985
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.023
20% Bioavailability (F20%):	0.001
30% Bioavailability (F30%):	0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.037
Plasma Protein Binding (PPB):	95.56670379638672%
Volume Distribution (VD):	0.569
Pgp-substrate:	6.626948833465576%

ADMET: Metabolism

CYP1A2-inhibitor:	0.128
CYP1A2-substrate:	0.967
CYP2C19-inhibitor:	0.624
CYP2C19-substrate:	0.606
CYP2C9-inhibitor:	0.688
CYP2C9-substrate:	0.955
CYP2D6-inhibitor:	0.101
CYP2D6-substrate:	0.538
CYP3A4-inhibitor:	0.179
CYP3A4-substrate:	0.479

ADMET: Excretion

Clearance (CL):	2.489
Half-life (T1/2):	0.112

ADMET: Toxicity

hERG Blockers:	0.015
Human Hepatotoxicity (H-HT):	0.377
Drug-inuced Liver Injury (DILI):	0.459
AMES Toxicity:	0.316
Rat Oral Acute Toxicity:	0.876
Maximum Recommended Daily Dose:	0.654
Skin Sensitization:	0.613
Carcinogencity:	0.206
Eye Corrosion:	0.003
Eye Irritation:	0.181
Respiratory Toxicity:	0.289

Download Data

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

Natural Product: NPC266330

Natural Product ID:	NPC266330
*Common Name:**	GBNCDYGXXWZSAO-IHWIRAEQSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GBNCDYGXXWZSAO-IHWIRAEQSA-N
Standard InCHI:	InChI=1S/C35H64O6/c1-3-4-5-6-7-8-9-10-14-17-23-31(37)33-25-26-34(41-33)32(38)24-19-18-22-30(36)21-16-13-11-12-15-20-29-27-28(2)40-35(29)39/h27-28,30-34,36-38H,3-26H2,1-2H3/t28-,30-,31+,32-,33-,34+/m1/s1
SMILES:	CCCCCCCCCCCC[C@@H]([C@H]1CC[C@@H]([C@@H](CCCC[C@@H](CCCCCCCC2=C[C@@H](C)OC2=O)O)O)O1)O
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:0003909] Fatty Acyls [CHEMONTID:0001334] Fatty alcohols [CHEMONTID:0002518] Annonaceous acetogenins

*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
NPO2253	Illicium jiadifengpi	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11975494]
NPO2558	Ceratodictyon spongiosum	Species	Lomentariaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19670881]
NPO7761	Laurencia majuscula	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8691206]
NPO1536	Lindera triloba	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7761	Laurencia majuscula	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3409	Goniothalamus leiocarpus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7450	Sida acuta	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2253	Illicium jiadifengpi	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1536	Lindera triloba	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2182	Athyrium filix-femina	Species	Athyriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7607	Ophiorrhiza pumila	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1093	Plumeria obtusa	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7450	Sida acuta	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7761	Laurencia majuscula	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3409	Goniothalamus leiocarpus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7450	Sida acuta	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3409	Goniothalamus leiocarpus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7450	Sida acuta	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3409	Goniothalamus leiocarpus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5796	Haplopappus foliosus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5262	Sargassum natans	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1536	Lindera triloba	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2558	Ceratodictyon spongiosum	Species	Lomentariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7761	Laurencia majuscula	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4276	Cupressus lindleyi	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4805	Balanophora papuana	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1693	Gnomonia fragariae	Species	Sydowiellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1878	Kunzea baxteri	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3114	Stylocheilus striatus	Species	Aplysiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2253	Illicium jiadifengpi	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6838	Senecio grisebachii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1093	Plumeria obtusa	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2182	Athyrium filix-femina	Species	Athyriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8060	Lethariella cashmeriana	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO274	Dendrobates viridis	Species	Dendrobatidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7607	Ophiorrhiza pumila	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2956	Echinometra oblonga	Species	Echinometridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11725	Cetonia aurata	Species	Scarabaeidae	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 NPC266330 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	168
0.1-0.2	1340
0.2-0.3	5732
0.3-0.4	15092
0.4-0.5	10262
0.5-0.6	6676
0.6-0.7	2691
0.7-0.8	547
0.8-0.85	19
0.85-0.9	26
0.9-0.95	102
0.95-1	42

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 NPC266330 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	146
0.1-0.2	2097
0.2-0.3	3947
0.3-0.4	2080
0.4-0.5	582
0.5-0.6	240
0.6-0.7	56
0.7-0.8	2
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