NPASS Compound

Structure

NPC281428 OpenBabel06302215222D 48 54 0 0 1 0 0 0 0 0999 V2000 -0.8416 4.0821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8797 3.4828 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8797 2.2840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8416 1.6846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8416 0.4859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6831 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6831 -0.9717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5247 -1.4576 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3662 -0.9717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3662 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.7041 1.1501 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9153 -0.5095 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8593 -1.2564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2404 -1.6784 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4191 -2.8638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5350 -3.3017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4819 -3.6112 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5247 0.4859 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8416 -1.4576 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.9717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8416 -1.4576 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8416 -2.6564 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6831 -0.9717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0401 -1.4639 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0401 -0.6137 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4546 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0580 0.6647 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0444 1.6977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6216 2.6859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7867 2.4751 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3874 1.6977 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0704 0.7160 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.6444 1.0122 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6072 1.6569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1470 2.0115 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7239 1.7213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1099 2.6562 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6497 3.0108 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5329 2.9464 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3878 0.1535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3670 -0.1172 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6831 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8416 0.4859 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 2.3828 0.1643 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7061 0.6790 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8416 -2.6564 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9179 4.0821 0.0000 C 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 2 48 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 44 2 0 0 0 0 5 6 1 0 0 0 0 6 18 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 19 1 0 0 0 0 8 9 1 1 0 0 0 8 14 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 1 0 0 0 10 12 1 0 0 0 0 10 18 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 1 0 0 0 15 16 2 0 0 0 0 15 17 1 0 0 0 0 19 20 2 0 0 0 0 19 47 1 0 0 0 0 20 44 1 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 23 24 2 0 0 0 0 24 25 1 0 0 0 0 25 40 1 0 0 0 0 25 26 1 0 0 0 0 25 45 1 1 0 0 0 27 26 1 1 0 0 0 27 28 1 0 0 0 0 27 42 1 0 0 0 0 28 29 1 0 0 0 0 28 30 1 0 0 0 0 28 31 1 0 0 0 0 31 32 1 0 0 0 0 32 33 1 6 0 0 0 32 40 1 0 0 0 0 32 42 1 0 0 0 0 33 34 1 0 0 0 0 34 35 2 0 0 0 0 35 36 1 0 0 0 0 35 37 1 0 0 0 0 37 38 2 0 0 0 0 37 39 1 0 0 0 0 40 41 2 0 0 0 0 42 23 1 6 0 0 0 42 43 1 0 0 0 0 43 44 1 0 0 0 0 45 46 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	658.31
Volume:	675.952
LogP:	7.76
LogD:	3.357
LogS:	-3.3
# Rotatable Bonds:	7
TPSA:	128.59
# H-Bond Aceptor:	9
# H-Bond Donor:	2
# Rings:	8
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.313
Synthetic Accessibility Score:	7.577
Fsp3:	0.564
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:	-5.025
MDCK Permeability:	1.7361369827995077e-05
Pgp-inhibitor:	0.784
Pgp-substrate:	0.704
Human Intestinal Absorption (HIA):	0.177
20% Bioavailability (F20%):	0.067
30% Bioavailability (F30%):	0.28

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.67
Plasma Protein Binding (PPB):	92.41996002197266%
Volume Distribution (VD):	1.381
Pgp-substrate:	5.23626708984375%

ADMET: Metabolism

CYP1A2-inhibitor:	0.023
CYP1A2-substrate:	0.977
CYP2C19-inhibitor:	0.022
CYP2C19-substrate:	0.87
CYP2C9-inhibitor:	0.265
CYP2C9-substrate:	0.247
CYP2D6-inhibitor:	0.011
CYP2D6-substrate:	0.087
CYP3A4-inhibitor:	0.631
CYP3A4-substrate:	0.932

ADMET: Excretion

Clearance (CL):	6.31
Half-life (T1/2):	0.027

ADMET: Toxicity

hERG Blockers:	0.063
Human Hepatotoxicity (H-HT):	0.953
Drug-inuced Liver Injury (DILI):	0.979
AMES Toxicity:	0.469
Rat Oral Acute Toxicity:	0.967
Maximum Recommended Daily Dose:	0.837
Skin Sensitization:	0.295
Carcinogencity:	0.961
Eye Corrosion:	0.003
Eye Irritation:	0.006
Respiratory Toxicity:	0.966

Download Data

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

Natural Product: NPC281428

Natural Product ID:	NPC281428
*Common Name:**	ADCLULBCVNNGML-RKMBXHABSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ADCLULBCVNNGML-RKMBXHABSA-N
Standard InCHI:	InChI=1S/C39H46O9/c1-19(2)10-11-23-31-27(24-16-36(8,46-31)14-13-22(24)20(3)4)30(41)28-29(40)25-17-37(45-9)18-26-35(6,7)48-38(34(37)44,15-12-21(5)33(42)43)39(25,26)47-32(23)28/h10,12,17,22,24,26,41H,3,11,13-16,18H2,1-2,4-9H3,(H,42,43)/b21-12-/t22-,24+,26+,36+,37+,38+,39-/m1/s1
SMILES:	CC(=CCc1c2c([C@H]3C[C@](C)(CC[C@@H]3C(=C)C)O2)c(c2C(=O)C3=C[C@@]4(C[C@H]5C(C)(C)O[C@@](C/C=C(/C)C(=O)O)(C4=O)[C@@]35Oc12)OC)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000123] Benzopyrans [CHEMONTID:0003410] 1-benzopyrans [CHEMONTID:0002817] Dibenzopyrans [CHEMONTID:0000200] Xanthenes [CHEMONTID:0000204] Xanthones [CHEMONTID:0003521] Pyranoxanthones

*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
NPO17342	Microcosmus vulgaris	Species	Pyuridae	Eukaryota	n.a.	n.a.	n.a.	PMID[10785429]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	fruit	n.a.	PMID[17117343]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	latex	n.a.	PMID[17117343]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	resin	n.a.	n.a.	PMID[19072548]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21486005]
NPO19429	Millettia auriculata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14692	Salix babylonica	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20295	Eclipta prostrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19429	Millettia auriculata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19508	Toxicodendron radicans	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20295	Eclipta prostrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14692	Salix babylonica	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14692	Salix babylonica	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20295	Eclipta prostrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20295	Eclipta prostrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28098	Rhizomnium pseudopunctatum	Species	Mniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19508	Toxicodendron radicans	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15765	Vernonanthura discolor	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11950	Ruscus hypoglossum	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20810	Lobaria adusta	Species	Lobariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13703	Croton discolor	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19300	Scleroderma tinctorium	Species	Sclerodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17093	Callitriche stagnalis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22632	Pteris glauca	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18593	Wrightia coccinea	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19429	Millettia auriculata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17342	Microcosmus vulgaris	Species	Pyuridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4477	Fasciola hepatica	Species	Fasciolidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19760	Fragaria chiloensis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14692	Salix babylonica	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20295	Eclipta prostrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18834	Scrophularia glabrata	Species	Scrophulariaceae	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 NPC281428 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	406
0.1-0.2	1643
0.2-0.3	3256
0.3-0.4	6731
0.4-0.5	10650
0.5-0.6	6859
0.6-0.7	5742
0.7-0.8	7137
0.8-0.85	204
0.85-0.9	20
0.9-0.95	33
0.95-1	16

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 NPC281428 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	357
0.1-0.2	988
0.2-0.3	1979
0.3-0.4	2688
0.4-0.5	1921
0.5-0.6	840
0.6-0.7	245
0.7-0.8	131
0.8-0.85	1
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