NPASS Compound

Structure

NPC35412 OpenBabel06302216212D 40 45 0 0 1 0 0 0 0 0999 V2000 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 0.0000 C 0 0 1 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 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -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 -1.7321 -1.0000 0.0000 C 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 -0.8660 -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 -2.5981 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -4.0000 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 -0.8660 0.5000 0.0000 C 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 2.0000 0.0000 C 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 1.7321 2.0000 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 3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 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 0.8660 0.5000 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 0.0000 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8301 2.3660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 8 1 0 0 0 0 3 4 1 0 0 0 0 4 20 2 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 5 9 2 0 0 0 0 6 7 1 1 0 0 0 6 8 1 0 0 0 0 9 10 1 0 0 0 0 9 40 1 0 0 0 0 10 15 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 20 1 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 13 18 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 18 19 1 0 0 0 0 20 21 1 0 0 0 0 21 36 2 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 24 35 2 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 26 33 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 6 0 0 0 28 30 1 0 0 0 0 28 39 1 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 31 33 1 0 0 0 0 33 34 2 0 0 0 0 34 35 1 0 0 0 0 34 38 1 0 0 0 0 35 36 1 0 0 0 0 36 37 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	544.21
Volume:	552.01
LogP:	6.38
LogD:	3.137
LogS:	-4.465
# Rotatable Bonds:	3
TPSA:	125.68
# H-Bond Aceptor:	8
# H-Bond Donor:	4
# Rings:	6
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.259
Synthetic Accessibility Score:	4.353
Fsp3:	0.344
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:	-5.348
MDCK Permeability:	9.697142559161875e-06
Pgp-inhibitor:	0.723
Pgp-substrate:	0.059
Human Intestinal Absorption (HIA):	0.807
20% Bioavailability (F20%):	0.001
30% Bioavailability (F30%):	0.139

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002
Plasma Protein Binding (PPB):	94.20128631591797%
Volume Distribution (VD):	0.435
Pgp-substrate:	7.327409267425537%

ADMET: Metabolism

CYP1A2-inhibitor:	0.177
CYP1A2-substrate:	0.957
CYP2C19-inhibitor:	0.415
CYP2C19-substrate:	0.242
CYP2C9-inhibitor:	0.741
CYP2C9-substrate:	0.843
CYP2D6-inhibitor:	0.017
CYP2D6-substrate:	0.321
CYP3A4-inhibitor:	0.103
CYP3A4-substrate:	0.191

ADMET: Excretion

Clearance (CL):	2.532
Half-life (T1/2):	0.067

ADMET: Toxicity

hERG Blockers:	0.018
Human Hepatotoxicity (H-HT):	0.519
Drug-inuced Liver Injury (DILI):	0.941
AMES Toxicity:	0.584
Rat Oral Acute Toxicity:	0.26
Maximum Recommended Daily Dose:	0.948
Skin Sensitization:	0.803
Carcinogencity:	0.426
Eye Corrosion:	0.003
Eye Irritation:	0.143
Respiratory Toxicity:	0.907

Download Data

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

Natural Product: NPC35412

Natural Product ID:	NPC35412
*Common Name:**	OFXNQLFWWFUNRK-ZTDVKWNISA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	OFXNQLFWWFUNRK-ZTDVKWNISA-N
Standard InCHI:	InChI=1S/C32H32O8/c1-14-8-20-24(15(2)40-14)30(35)28-21(10-18(38-4)11-23(28)39-5)27(20)19-7-6-16-9-17-12-32(3,37)13-22(33)25(17)31(36)26(16)29(19)34/h6-7,9-11,14-15,34-37H,8,12-13H2,1-5H3/t14-,15+,32+/m0/s1
SMILES:	C[C@H]1Cc2c([C@@H](C)O1)c(c1c(cc(cc1OC)OC)c2c1ccc2cc3C[C@](C)(CC(=O)c3c(c2c1O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0001610] Arylnaphthalene lignans

*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
NPO9402	Morus mongolica	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11429996]
NPO17807	Dysosma versipellis	Species	Berberidaceae	Eukaryota	Roots	Panan, Zhejiang Province, China	2004-MAY	PMID[17256902]
NPO17807	Dysosma versipellis	Species	Berberidaceae	Eukaryota	n.a.	root	n.a.	PMID[17256902]
NPO28260	Senna alexandrina	Species	Fabaceae	Eukaryota	n.a.	seed	n.a.	PMID[17345316]
NPO17807	Dysosma versipellis	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25712646]
NPO20676	Spathelia sorbifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3598592]
NPO17807	Dysosma versipellis	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9402	Morus mongolica	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18543	Mercurialis annua	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28260	Senna alexandrina	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2140	Botryococcus braunii	Species	Botryococcaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9402	Morus mongolica	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18543	Mercurialis annua	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17807	Dysosma versipellis	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17807	Dysosma versipellis	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9402	Morus mongolica	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28260	Senna alexandrina	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO2997	Aloe africana	Species	Xanthorrhoeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3035	Karwinskia humboldtiana	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20676	Spathelia sorbifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18543	Mercurialis annua	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15300	Bipolaris zeicola	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9402	Morus mongolica	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17807	Dysosma versipellis	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2997	Aloe africana	Species	Xanthorrhoeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7706	Bartlettina karwinskiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2140	Botryococcus braunii	Species	Botryococcaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28260	Senna alexandrina	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9708	Aster verticillatus	Species	Asteraceae	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 NPC35412 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	420
0.1-0.2	1669
0.2-0.3	3362
0.3-0.4	9436
0.4-0.5	9424
0.5-0.6	3718
0.6-0.7	5721
0.7-0.8	5873
0.8-0.85	2185
0.85-0.9	777
0.9-0.95	111
0.95-1	1

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 NPC35412 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	371
0.1-0.2	1001
0.2-0.3	1492
0.3-0.4	2635
0.4-0.5	1958
0.5-0.6	1098
0.6-0.7	394
0.7-0.8	162
0.8-0.85	30
0.85-0.9	8
0.9-0.95	0
0.95-1	1

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