NPASS Compound

Structure

NPC259008 OpenBabel06302215092D 44 47 0 0 1 0 0 0 0 0999 V2000 -5.2157 0.4672 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7500 -0.3398 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8183 -0.3401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3522 0.4667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4205 0.4664 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6137 0.0003 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4208 -0.4655 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6141 -0.9315 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4211 -1.3972 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6624 -2.2971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5624 -2.5381 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8038 -3.4380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2211 -1.8791 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8070 -1.3976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.9318 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -1.8633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5388 -2.6232 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1502 -3.4697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6890 -4.2296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7773 -3.5564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8068 -0.4662 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8070 0.4657 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6143 0.9315 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6145 1.8633 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4213 0.4653 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2285 0.9311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0355 0.4649 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0353 -0.4671 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2280 -0.9328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4210 -0.4666 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6138 -0.9324 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8421 -0.9331 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8425 0.9306 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0001 0.9316 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0001 1.8634 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8067 0.4660 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6132 0.9320 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6997 1.8594 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5461 2.2483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6326 3.1758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3061 1.7097 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8070 0.4658 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2161 -1.1466 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 44 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 36 1 0 0 0 0 6 7 1 1 0 0 0 6 8 1 0 0 0 0 8 9 1 1 0 0 0 8 14 1 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 11 13 1 0 0 0 0 14 15 1 0 0 0 0 15 42 1 0 0 0 0 15 16 1 1 0 0 0 15 21 1 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 18 20 1 0 0 0 0 21 31 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 22 34 1 0 0 0 0 23 24 2 0 0 0 0 23 25 1 0 0 0 0 25 30 2 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 27 28 1 0 0 0 0 27 33 1 0 0 0 0 28 29 2 0 0 0 0 28 32 1 0 0 0 0 29 30 1 0 0 0 0 30 31 1 0 0 0 0 34 35 2 0 0 0 0 34 36 1 0 0 0 0 36 37 1 1 0 0 0 36 42 1 0 0 0 0 37 38 1 0 0 0 0 38 39 2 0 0 0 0 39 40 1 0 0 0 0 39 41 1 0 0 0 0 42 43 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	478.19
Volume:	447.241
LogP:	-0.375
LogD:	0.204
LogS:	-0.597
# Rotatable Bonds:	5
TPSA:	159.82
# H-Bond Aceptor:	10
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.252
Synthetic Accessibility Score:	4.886
Fsp3:	0.857
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:	-5.5
MDCK Permeability:	2.409360240562819e-05
Pgp-inhibitor:	0.019
Pgp-substrate:	0.211
Human Intestinal Absorption (HIA):	0.903
20% Bioavailability (F20%):	0.358
30% Bioavailability (F30%):	0.907

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.04
Plasma Protein Binding (PPB):	82.45048522949219%
Volume Distribution (VD):	1.016
Pgp-substrate:	12.677224159240723%

ADMET: Metabolism

CYP1A2-inhibitor:	0.005
CYP1A2-substrate:	0.158
CYP2C19-inhibitor:	0.018
CYP2C19-substrate:	0.513
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.068
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.114
CYP3A4-inhibitor:	0.012
CYP3A4-substrate:	0.054

ADMET: Excretion

Clearance (CL):	2.345
Half-life (T1/2):	0.515

ADMET: Toxicity

hERG Blockers:	0.05
Human Hepatotoxicity (H-HT):	0.806
Drug-inuced Liver Injury (DILI):	0.183
AMES Toxicity:	0.311
Rat Oral Acute Toxicity:	0.777
Maximum Recommended Daily Dose:	0.965
Skin Sensitization:	0.937
Carcinogencity:	0.497
Eye Corrosion:	0.053
Eye Irritation:	0.315
Respiratory Toxicity:	0.984

Download Data

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

Natural Product: NPC259008

Natural Product ID:	NPC259008
*Common Name:**	FYLGKUMBFTYCET-HYOCDBLYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	FYLGKUMBFTYCET-HYOCDBLYSA-N
Standard InCHI:	InChI=1S/C38H48O6/c1-22(2)11-10-16-36(9)26(13-12-23(3)4)21-37(17-14-24(5)6)34-31(33(42)38(36,35(37)43)18-15-25(7)8)32(41)27-19-28(39)29(40)20-30(27)44-34/h11-12,14-15,19-20,26,39-40H,10,13,16-18,21H2,1-9H3/t26-,36+,37+,38-/m1/s1
SMILES:	CC(=CCC[C@@]1(C)[C@H](CC=C(C)C)C[C@@]2(CC=C(C)C)c3c(c(=O)c4cc(c(cc4o3)O)O)C(=O)[C@]1(CC=C(C)C)C2=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	102164366
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000123] Benzopyrans [CHEMONTID:0003410] 1-benzopyrans [CHEMONTID:0002817] Dibenzopyrans [CHEMONTID:0000200] Xanthenes [CHEMONTID:0000204] Xanthones

*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
NPO6536	Marrubium velutinum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17287127]
NPO6536	Marrubium velutinum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6536	Marrubium velutinum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1330	Stachybotrys alternans	Species	Stachybotryaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2382	Nicotiana excelsior	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO769	Eria elata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24463	Linum corymbulosum	Species	Linaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12849	Lagerstroemia subcostata	Species	Lythraceae	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 NPC259008 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	472
0.1-0.2	1814
0.2-0.3	3652
0.3-0.4	9124
0.4-0.5	9410
0.5-0.6	4165
0.6-0.7	5457
0.7-0.8	5776
0.8-0.85	2066
0.85-0.9	685
0.9-0.95	69
0.95-1	7

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 NPC259008 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	415
0.1-0.2	985
0.2-0.3	1825
0.3-0.4	2691
0.4-0.5	1882
0.5-0.6	869
0.6-0.7	335
0.7-0.8	124
0.8-0.85	22
0.85-0.9	2
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