NPASS Compound

Structure

NPC3973 OpenBabel06302216092D 23 26 0 0 0 0 0 0 0 0999 V2000 -2.1472 -2.7753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6702 -1.9386 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8387 -1.4526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0045 -1.9342 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8291 -1.4537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8341 -0.4816 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6706 0.0038 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6697 0.9657 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8356 1.4473 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8409 2.4142 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0075 0.9727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8466 1.4572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6839 0.9589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6882 -0.0004 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5200 -0.4782 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8725 -1.3704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8214 -1.5113 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4179 -0.7600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0654 0.1323 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1165 0.2731 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8491 -0.4848 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 -0.0049 -2.8989 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 21 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 23 1 0 0 0 0 5 6 1 0 0 0 0 6 22 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 11 22 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 14 21 1 0 0 0 0 15 20 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 21 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	302.09
Volume:	320.256
LogP:	4.54
LogD:	3.666
LogS:	-5.921
# Rotatable Bonds:	2
TPSA:	46.53
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.761
Synthetic Accessibility Score:	2.496
Fsp3:	0.05
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.913
MDCK Permeability:	1.4686241229355801e-05
Pgp-inhibitor:	0.4
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.005
30% Bioavailability (F30%):	0.236

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.131
Plasma Protein Binding (PPB):	99.87445831298828%
Volume Distribution (VD):	0.419
Pgp-substrate:	1.0241162776947021%

ADMET: Metabolism

CYP1A2-inhibitor:	0.977
CYP1A2-substrate:	0.659
CYP2C19-inhibitor:	0.944
CYP2C19-substrate:	0.074
CYP2C9-inhibitor:	0.849
CYP2C9-substrate:	0.926
CYP2D6-inhibitor:	0.711
CYP2D6-substrate:	0.894
CYP3A4-inhibitor:	0.557
CYP3A4-substrate:	0.184

ADMET: Excretion

Clearance (CL):	3.707
Half-life (T1/2):	0.263

ADMET: Toxicity

hERG Blockers:	0.325
Human Hepatotoxicity (H-HT):	0.188
Drug-inuced Liver Injury (DILI):	0.884
AMES Toxicity:	0.853
Rat Oral Acute Toxicity:	0.456
Maximum Recommended Daily Dose:	0.899
Skin Sensitization:	0.935
Carcinogencity:	0.841
Eye Corrosion:	0.01
Eye Irritation:	0.958
Respiratory Toxicity:	0.776

Download Data

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

Natural Product: NPC3973

Natural Product ID:	NPC3973
*Common Name:**	YBNVZTRILGRXEI-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YBNVZTRILGRXEI-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C20H14O3/c1-23-20-17(22)11-13-7-10-16(21)15-9-8-14(19(20)18(13)15)12-5-3-2-4-6-12/h2-11,22H,1H3
SMILES:	COc1c(cc2C=CC(=O)c3ccc(c4ccccc4)c1c23)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	85730238
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000023] Naphthalenes [CHEMONTID:0002044] Phenylnaphthalenes

*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
NPO22441	Senna spectabilis	Species	Fabaceae	Eukaryota	flowers	n.a.	n.a.	PMID[30413343]
NPO23044	Aesculus hippocastanum	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3783160]
NPO23044	Aesculus hippocastanum	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10654	Lindera obtusiloba	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23044	Aesculus hippocastanum	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10654	Lindera obtusiloba	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16782	Andrographis viscosula	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10654	Lindera obtusiloba	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23044	Aesculus hippocastanum	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10654	Lindera obtusiloba	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO16548	Chenopodium formosanum	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10654	Lindera obtusiloba	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5869	Anthocercis albicans	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22441	Senna spectabilis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10984	Euclea crispa	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11360	Tiliacora racemosa	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18427	Axinella agnata	Species	Axinellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17900	Iotrochota birotulata	Species	Iotrochotidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3096	Verbascum laxum	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10064	Diospyros canaliculata	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19091	Bacterium from	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO23044	Aesculus hippocastanum	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16782	Andrographis viscosula	Species	Acanthaceae	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 NPC3973 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	402
0.1-0.2	1801
0.2-0.3	4143
0.3-0.4	11545
0.4-0.5	6364
0.5-0.6	3691
0.6-0.7	7064
0.7-0.8	6937
0.8-0.85	652
0.85-0.9	68
0.9-0.95	28
0.95-1	2

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 NPC3973 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	385
0.1-0.2	1048
0.2-0.3	1334
0.3-0.4	2637
0.4-0.5	1917
0.5-0.6	1121
0.6-0.7	559
0.7-0.8	142
0.8-0.85	7
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