NPASS Compound

Structure

NPC185378 OpenBabel06302216162D 33 35 0 0 1 0 0 0 0 0999 V2000 -1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 1.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.2601 2.2601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2382 2.4680 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5388 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5388 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0388 1.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0388 1.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5388 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0388 -0.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0388 -0.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5388 -1.2321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0388 -2.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5388 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0388 -0.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0388 -0.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5388 -1.2321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5388 -1.2321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0388 -2.0981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5388 2.2321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5388 2.2321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 -0.3090 0.0000 O 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 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 33 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 10 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 10 11 2 0 0 0 0 11 33 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 1 0 0 0 12 15 1 0 0 0 0 13 14 1 0 0 0 0 15 16 1 6 0 0 0 15 32 1 0 0 0 0 16 21 2 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 30 1 0 0 0 0 19 20 2 0 0 0 0 19 24 1 0 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 22 23 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 25 28 1 0 0 0 0 26 27 1 0 0 0 0 28 29 1 0 0 0 0 30 31 1 0 0 0 0 32 33 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	464.2
Volume:	461.284
LogP:	1.062
LogD:	1.548
LogS:	-3.433
# Rotatable Bonds:	12
TPSA:	127.07
# H-Bond Aceptor:	9
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.37
Synthetic Accessibility Score:	3.627
Fsp3:	0.5
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:	-5.048
MDCK Permeability:	6.60704608890228e-05
Pgp-inhibitor:	0.705
Pgp-substrate:	0.026
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.011
30% Bioavailability (F30%):	0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.258
Plasma Protein Binding (PPB):	36.898193359375%
Volume Distribution (VD):	0.895
Pgp-substrate:	29.745298385620117%

ADMET: Metabolism

CYP1A2-inhibitor:	0.024
CYP1A2-substrate:	0.21
CYP2C19-inhibitor:	0.015
CYP2C19-substrate:	0.881
CYP2C9-inhibitor:	0.016
CYP2C9-substrate:	0.376
CYP2D6-inhibitor:	0.012
CYP2D6-substrate:	0.232
CYP3A4-inhibitor:	0.592
CYP3A4-substrate:	0.893

ADMET: Excretion

Clearance (CL):	5.307
Half-life (T1/2):	0.729

ADMET: Toxicity

hERG Blockers:	0.216
Human Hepatotoxicity (H-HT):	0.403
Drug-inuced Liver Injury (DILI):	0.087
AMES Toxicity:	0.058
Rat Oral Acute Toxicity:	0.136
Maximum Recommended Daily Dose:	0.233
Skin Sensitization:	0.546
Carcinogencity:	0.061
Eye Corrosion:	0.003
Eye Irritation:	0.009
Respiratory Toxicity:	0.004

Download Data

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

Natural Product: NPC185378

Natural Product ID:	NPC185378
*Common Name:**	UDNVBKBWANAIGZ-GCJKJVERSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	UDNVBKBWANAIGZ-GCJKJVERSA-N
Standard InCHI:	InChI=1S/C24H32O9/c1-29-19-8-14(5-4-6-25)7-17-18(13-28)22(33-23(17)19)15-9-20(30-2)24(21(10-15)31-3)32-16(11-26)12-27/h7-10,16,18,22,25-28H,4-6,11-13H2,1-3H3/t18-,22+/m1/s1
SMILES:	COc1cc(CCCO)cc2[C@@H](CO)[C@H](c3cc(c(c(c3)OC)OC(CO)CO)OC)Oc12
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	71591634
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0003405] 2-arylbenzofuran flavonoids

*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
NPO16693	Byrsonima crassifolia	Species	Malpighiaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO16693	Byrsonima crassifolia	Species	Malpighiaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO16693	Byrsonima crassifolia	Species	Malpighiaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO9141	Epimedium wushanense	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26304	Hymenocallis littoralis	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9141	Epimedium wushanense	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15954	Pyrenula japonica	Species	Pyrenulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26304	Hymenocallis littoralis	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16326	Scopolia parviflora	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9141	Epimedium wushanense	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11755	Banisteriopsis caapi	Species	Malpighiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17600	Gnathotrichus sulcatus	Species	Curculionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15594	Aplidiopsis confluata	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO16326	Scopolia parviflora	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17444	Gleichenia japonica	Species	Gleicheniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14001	Ceroplastes pseudoceriferus	Species	Coccidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15954	Pyrenula japonica	Species	Pyrenulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5016	Glossogyne tenuifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12630	Senecio oxyodontus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26304	Hymenocallis littoralis	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17757	Plectranthus saccatus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15740	Garcinia purpurea	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10751	Bothriocline laxa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14507.1	Quercus ithaburensis subsp. macrolepis	Subspecies	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11280	Aphanoascus terreus	Species	Onygenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16049	Cryptocarya pleurosperma	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO619	Ankistrodesmus braunii	Species	Selenastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16210	Androcymbium palaestinum	Species	Colchicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17141	Lonchocarpus longistylus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16693	Byrsonima crassifolia	Species	Malpighiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9141	Epimedium wushanense	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18071	Euryops pedunculatus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17917	Thamnophis sirtalis	Species	Colubridae	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 NPC185378 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	423
0.1-0.2	1429
0.2-0.3	4024
0.3-0.4	10533
0.4-0.5	8201
0.5-0.6	3985
0.6-0.7	7083
0.7-0.8	5313
0.8-0.85	972
0.85-0.9	602
0.9-0.95	127
0.95-1	5

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 NPC185378 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	336
0.1-0.2	867
0.2-0.3	1956
0.3-0.4	2698
0.4-0.5	1612
0.5-0.6	898
0.6-0.7	605
0.7-0.8	168
0.8-0.85	7
0.85-0.9	3
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