NPASS Compound

Structure

NPC295776 OpenBabel06302215282D 42 48 0 0 1 0 0 0 0 0999 V2000 -3.3952 1.6218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6512 1.1510 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6869 0.2712 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4667 -0.1377 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9430 -0.1996 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9787 -1.0793 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1632 0.2093 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4192 -0.2615 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4762 -0.7524 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1279 -1.1029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3633 -1.0492 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9770 -1.5994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3634 -0.6296 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3635 0.2101 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3632 0.6298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0904 0.2102 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5443 0.2103 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.2715 0.6300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9983 0.2104 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.9983 -0.6293 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.2716 -1.0490 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.2717 -1.8882 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9985 -2.3077 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 3.9986 -3.1469 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7254 -3.5664 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.7255 -4.4469 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4522 -3.1467 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4521 -2.3075 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7252 -1.8880 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.7251 -1.0488 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1653 -0.2863 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6056 -1.0487 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5444 -0.6294 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.8172 -1.0491 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0905 -0.6295 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7270 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.1099 1.7575 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5444 -1.4536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7121 -0.2171 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7120 0.6226 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5443 1.0345 0.0000 O 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 3 4 1 0 0 0 0 3 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 8 7 1 6 0 0 0 8 9 1 0 0 0 0 8 37 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 35 1 0 0 0 0 11 12 1 6 0 0 0 11 13 1 0 0 0 0 13 14 1 6 0 0 0 13 37 1 0 0 0 0 14 15 1 0 0 0 0 16 15 1 1 0 0 0 16 17 1 0 0 0 0 16 35 1 0 0 0 0 17 33 1 0 0 0 0 17 18 1 0 0 0 0 17 42 1 1 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 19 41 1 6 0 0 0 20 30 1 0 0 0 0 20 21 1 0 0 0 0 20 40 1 1 0 0 0 21 22 1 1 0 0 0 21 33 1 0 0 0 0 22 23 1 0 0 0 0 23 29 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 6 0 0 0 25 27 1 0 0 0 0 27 28 1 0 0 0 0 29 28 1 6 0 0 0 29 30 1 0 0 0 0 30 31 1 1 0 0 0 30 32 1 0 0 0 0 33 34 1 0 0 0 0 33 39 1 1 0 0 0 35 34 1 1 0 0 0 35 36 1 0 0 0 0 36 37 1 0 0 0 0 37 38 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	591.34
Volume:	586.969
LogP:	2.187
LogD:	1.447
LogS:	-3.808
# Rotatable Bonds:	3
TPSA:	160.15
# H-Bond Aceptor:	10
# H-Bond Donor:	6
# Rings:	7
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.202
Synthetic Accessibility Score:	7.191
Fsp3:	0.906
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
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:	-5.002
MDCK Permeability:	4.7420046030310914e-05
Pgp-inhibitor:	0.442
Pgp-substrate:	0.991
Human Intestinal Absorption (HIA):	0.742
20% Bioavailability (F20%):	0.085
30% Bioavailability (F30%):	0.812

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.358
Plasma Protein Binding (PPB):	71.02045440673828%
Volume Distribution (VD):	0.715
Pgp-substrate:	23.638816833496094%

ADMET: Metabolism

CYP1A2-inhibitor:	0.008
CYP1A2-substrate:	0.65
CYP2C19-inhibitor:	0.026
CYP2C19-substrate:	0.363
CYP2C9-inhibitor:	0.028
CYP2C9-substrate:	0.068
CYP2D6-inhibitor:	0.118
CYP2D6-substrate:	0.34
CYP3A4-inhibitor:	0.386
CYP3A4-substrate:	0.223

ADMET: Excretion

Clearance (CL):	3.15
Half-life (T1/2):	0.445

ADMET: Toxicity

hERG Blockers:	0.108
Human Hepatotoxicity (H-HT):	0.815
Drug-inuced Liver Injury (DILI):	0.041
AMES Toxicity:	0.034
Rat Oral Acute Toxicity:	0.805
Maximum Recommended Daily Dose:	0.931
Skin Sensitization:	0.717
Carcinogencity:	0.939
Eye Corrosion:	0.003
Eye Irritation:	0.015
Respiratory Toxicity:	0.975

Download Data

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

Natural Product: NPC295776

Natural Product ID:	NPC295776
*Common Name:**	DBUCFOVFALNEOO-WEWWNPNQSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DBUCFOVFALNEOO-WEWWNPNQSA-N
Standard InCHI:	InChI=1S/C32H49NO9/c1-6-18(3)25(35)41-24-11-12-26(4)19-8-9-20-28(37)13-23(34)31(39)21(29(28,38)16-30(20,26)42-32(19,24)40)15-33-14-17(2)7-10-22(33)27(31,5)36/h6,17,19-24,34,36-40H,7-16H2,1-5H3/b18-6-/t17-,19-,20-,21-,22-,23-,24-,26-,27+,28+,29+,30+,31-,32+/m0/s1
SMILES:	C/C=C(/C)C(=O)O[C@H]1CC[C@@]2(C)[C@@H]3CC[C@H]4[C@@]5(C[C@@H]([C@]6([C@@H](CN7C[C@@H](C)CC[C@H]7[C@@]6(C)O)[C@@]5(C[C@]24O[C@@]13O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	45006071
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002724] Steroidal alkaloids [CHEMONTID:0002729] Cerveratrum-type alkaloids

*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
NPO14417	Iris tectorum	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10075762]
NPO4373	Phyllanthus acuminatus	Species	Phyllanthaceae	Eukaryota	Roots	n.a.	n.a.	PMID[2089115]
NPO14417	Iris tectorum	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24433009]
NPO14417	Iris tectorum	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28032759]
NPO2634	Tetrapleura tetraptera	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8289059]
NPO14417	Iris tectorum	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4373	Phyllanthus acuminatus	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10815	Uncaria borneensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4373	Phyllanthus acuminatus	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14417	Iris tectorum	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10815	Uncaria borneensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4373	Phyllanthus acuminatus	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14417	Iris tectorum	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14417	Iris tectorum	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO10815	Uncaria borneensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9373	Sigmadocia symbiotica	Species	Chalinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1718	Sarcodontia setosa	Species	Meruliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2634	Tetrapleura tetraptera	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20796	Stemonoporus canaliculatus	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14417	Iris tectorum	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7675	Perezia cuernavacana	Species	Pereziidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1968	Delphinium ternatum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8057	Bulnesia retama	Species	Zygophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4148	Artemisia spicigera	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO612	Pteronia stricta	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9242	Bauhinia manca	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4373	Phyllanthus acuminatus	Species	Phyllanthaceae	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 NPC295776 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	207
0.1-0.2	1727
0.2-0.3	7146
0.3-0.4	16705
0.4-0.5	9579
0.5-0.6	5077
0.6-0.7	2017
0.7-0.8	228
0.8-0.85	4
0.85-0.9	7
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 NPC295776 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	134
0.1-0.2	1155
0.2-0.3	4100
0.3-0.4	2725
0.4-0.5	774
0.5-0.6	219
0.6-0.7	30
0.7-0.8	13
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