NPASS Compound

Structure

NPC210477 OpenBabel06302215342D 43 49 0 0 1 0 0 0 0 0999 V2000 2.3821 4.2830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3821 3.2830 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.2481 2.7830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2481 1.7830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3821 1.2830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3821 0.2830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5161 -0.2170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6501 0.2830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6501 1.2830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5161 1.7830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5161 2.7830 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1804 3.4075 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6601 3.8891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2094 4.7248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5218 5.4272 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4303 5.1829 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6948 4.2362 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0116 4.1757 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3826 4.0641 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9772 3.6780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4142 3.1197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6463 2.4497 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6483 1.7407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7880 2.0448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4894 2.9069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4199 1.0695 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9860 0.5088 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3936 0.1194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4346 -0.5884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0681 -0.9068 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6605 -0.5174 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6195 0.1904 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.1275 -1.0087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6101 -0.9528 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3997 -0.4768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7067 -0.0566 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5946 -0.3696 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0201 -1.7602 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4243 -2.6749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1298 5.8975 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5161 -1.2170 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3821 -1.7170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 11 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 10 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 42 1 0 0 0 0 8 37 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 1 0 0 0 12 13 1 0 0 0 0 13 18 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 41 1 0 0 0 0 17 18 1 0 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 20 25 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 23 26 1 0 0 0 0 24 25 1 0 0 0 0 27 26 1 1 0 0 0 27 28 1 0 0 0 0 27 32 1 0 0 0 0 28 36 2 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 29 33 2 0 0 0 0 30 31 1 0 0 0 0 31 32 1 0 0 0 0 33 34 1 0 0 0 0 34 35 2 0 0 0 0 34 39 1 0 0 0 0 35 36 1 0 0 0 0 35 38 1 0 0 0 0 36 37 1 0 0 0 0 39 40 1 0 0 0 0 42 43 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	886.57
Volume:	923.026
LogP:	5.005
LogD:	3.751
LogS:	-3.027
# Rotatable Bonds:	37
TPSA:	231.13
# H-Bond Aceptor:	15
# H-Bond Donor:	7
# Rings:	2
# Heavy Atoms:	15

MedChem Properties

QED Drug-Likeness Score:	0.024
Synthetic Accessibility Score:	5.353
Fsp3:	0.83
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	2
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.293
MDCK Permeability:	1.7783964722184464e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.294
Human Intestinal Absorption (HIA):	0.68
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.007
Plasma Protein Binding (PPB):	99.92415618896484%
Volume Distribution (VD):	1.211
Pgp-substrate:	1.161062479019165%

ADMET: Metabolism

CYP1A2-inhibitor:	0.005
CYP1A2-substrate:	0.059
CYP2C19-inhibitor:	0.02
CYP2C19-substrate:	0.04
CYP2C9-inhibitor:	0.102
CYP2C9-substrate:	0.926
CYP2D6-inhibitor:	0.042
CYP2D6-substrate:	0.042
CYP3A4-inhibitor:	0.32
CYP3A4-substrate:	0.011

ADMET: Excretion

Clearance (CL):	1.832
Half-life (T1/2):	0.923

ADMET: Toxicity

hERG Blockers:	0.844
Human Hepatotoxicity (H-HT):	0.133
Drug-inuced Liver Injury (DILI):	0.017
AMES Toxicity:	0.821
Rat Oral Acute Toxicity:	0.005
Maximum Recommended Daily Dose:	0.012
Skin Sensitization:	0.972
Carcinogencity:	0.263
Eye Corrosion:	0.003
Eye Irritation:	0.009
Respiratory Toxicity:	0.162

Download Data

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

Natural Product: NPC210477

Natural Product ID:	NPC210477
*Common Name:**	UQNHXSCEVWBPSL-RRPNLBNLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	UQNHXSCEVWBPSL-RRPNLBNLSA-N
Standard InCHI:	InChI=1S/C35H36N2O6/c1-37-13-11-22-17-30(40-2)31-19-25(22)27(37)15-21-6-9-28(38)29(16-21)42-24-7-4-20(5-8-24)14-26-33-23(10-12-36-26)18-32(41-3)34(39)35(33)43-31/h4-9,16-19,26-27,36,38-39H,10-15H2,1-3H3/t26-,27+/m0/s1
SMILES:	CN1CCc2cc(c3cc2[C@H]1Cc1ccc(c(c1)Oc1ccc(cc1)C[C@H]1c2c(CCN1)cc(c(c2O3)O)OC)O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	46872348
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds

*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
NPO10590.1	Morus alba var. multicaulis	Varieties	Moraceae	Eukaryota	Fruits	Zhenjiang, Jiangsu Province, China		PMID[23060696]
NPO5921	Xestospongia caycedoi	Species	Petrosiidae	Eukaryota	n.a.	Fijian	n.a.	PMID[3430171]
NPO6484	Alstonia venenata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10681	Pycnarrhena longifolia	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6484	Alstonia venenata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10681	Pycnarrhena longifolia	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6484	Alstonia venenata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10681	Pycnarrhena longifolia	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10590.1	Morus alba var. multicaulis	Varieties	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7219	Vernonia potamophila	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2307	Trigonella corniculata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6484	Alstonia venenata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4954.1	Eleutherococcus divaricatus var. chiisanensis	Varieties	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16133	Hymenoxys richardsonii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7772	Conyza aegyptiaca	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1357	Cussonia paniculata	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO279	Mahonia morrisonensis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO5485	Rothmannia globosa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7938	Merendera manissadjianii	Species	Colchicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5921	Xestospongia caycedoi	Species	Petrosiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7284	Machilus glaucescens	Species	Lauraceae	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 NPC210477 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	373
0.1-0.2	1900
0.2-0.3	9591
0.3-0.4	8630
0.4-0.5	6149
0.5-0.6	9641
0.6-0.7	5278
0.7-0.8	841
0.8-0.85	159
0.85-0.9	48
0.9-0.95	44
0.95-1	43

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 NPC210477 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	197
0.1-0.2	749
0.2-0.3	1199
0.3-0.4	2143
0.4-0.5	2534
0.5-0.6	1551
0.6-0.7	650
0.7-0.8	116
0.8-0.85	5
0.85-0.9	0
0.9-0.95	4
0.95-1	2

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