NPASS Compound

Structure

NPC44720 OpenBabel06302215212D 37 42 0 0 1 0 0 0 0 0999 V2000 -4.9467 4.9099 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8144 4.4091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8145 3.4072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9470 2.9062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9471 1.9044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7717 1.4284 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7718 0.4763 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5964 0.0004 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4209 0.4765 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4208 1.4286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.9216 2.2963 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.4226 1.4287 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5962 1.9046 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9473 0.0002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1227 0.4761 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2982 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2983 -1.0018 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4736 0.4759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6492 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8244 0.4760 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8247 1.4280 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6491 1.9039 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4735 1.4281 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2980 1.9042 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1226 1.4282 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6490 2.8560 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8245 3.3322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0001 2.8562 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.9039 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8244 1.4280 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 0.2542 -0.9487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8506 -0.4911 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8504 3.3474 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4996 3.3471 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9474 -1.0017 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6820 4.9101 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 37 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 25 2 0 0 0 0 5 6 1 0 0 0 0 6 13 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 14 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 10 12 1 0 0 0 0 10 13 1 0 0 0 0 14 15 2 0 0 0 0 14 36 1 0 0 0 0 15 25 1 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 18 1 0 0 0 0 18 23 2 0 0 0 0 18 19 1 0 0 0 0 20 19 1 1 0 0 0 20 21 1 0 0 0 0 20 31 1 0 0 0 0 21 29 2 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 22 26 2 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 26 27 1 0 0 0 0 26 35 1 0 0 0 0 27 28 2 0 0 0 0 28 29 1 0 0 0 0 28 34 1 0 0 0 0 29 30 1 0 0 0 0 30 31 1 0 0 0 0 31 32 1 0 0 0 0 31 33 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	502.2
Volume:	511.264
LogP:	7.799
LogD:	4.401
LogS:	-1.782
# Rotatable Bonds:	2
TPSA:	109.36
# H-Bond Aceptor:	7
# H-Bond Donor:	3
# Rings:	6
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.364
Synthetic Accessibility Score:	4.303
Fsp3:	0.367
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.99
MDCK Permeability:	1.5990119209163822e-05
Pgp-inhibitor:	0.983
Pgp-substrate:	0.008
Human Intestinal Absorption (HIA):	0.544
20% Bioavailability (F20%):	0.005
30% Bioavailability (F30%):	0.006

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002
Plasma Protein Binding (PPB):	99.03987121582031%
Volume Distribution (VD):	0.539
Pgp-substrate:	3.4702322483062744%

ADMET: Metabolism

CYP1A2-inhibitor:	0.177
CYP1A2-substrate:	0.295
CYP2C19-inhibitor:	0.328
CYP2C19-substrate:	0.067
CYP2C9-inhibitor:	0.814
CYP2C9-substrate:	0.909
CYP2D6-inhibitor:	0.057
CYP2D6-substrate:	0.131
CYP3A4-inhibitor:	0.155
CYP3A4-substrate:	0.134

ADMET: Excretion

Clearance (CL):	1.298
Half-life (T1/2):	0.07

ADMET: Toxicity

hERG Blockers:	0.007
Human Hepatotoxicity (H-HT):	0.97
Drug-inuced Liver Injury (DILI):	0.974
AMES Toxicity:	0.111
Rat Oral Acute Toxicity:	0.975
Maximum Recommended Daily Dose:	0.915
Skin Sensitization:	0.452
Carcinogencity:	0.636
Eye Corrosion:	0.003
Eye Irritation:	0.065
Respiratory Toxicity:	0.653

Download Data

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

Natural Product: NPC44720

Natural Product ID:	NPC44720
*Common Name:**	CYONWSIQFYQFOS-KRWDZBQOSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CYONWSIQFYQFOS-KRWDZBQOSA-N
Standard InCHI:	InChI=1S/C30H30O7/c1-13(2)7-8-15-25-14(9-10-29(3,4)36-25)23(33)22-24(34)16-11-17-20-21(27(16)35-26(15)22)18(31)12-19(32)28(20)37-30(17,5)6/h7,9-10,12,17,31-33H,8,11H2,1-6H3/t17-/m0/s1
SMILES:	CC(=CCc1c2c(C=CC(C)(C)O2)c(c2c(=O)c3C[C@H]4c5c(-c3oc12)c(cc(c5OC4(C)C)O)O)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
NPO28803	Artocarpus chama	Species	Moraceae	Eukaryota	n.a.	root	n.a.	PMID[15165133]
NPO12348	Chrysosplenium grayanum	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1955888]
NPO6876	Ixora coccinea	Species	Rubiaceae	Eukaryota	aerial parts	collected on the campus of Kaohsiung Medical University, Taiwan	2007-Oct	PMID[21106454]
NPO28969	Solanum sarrachoides	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12348	Chrysosplenium grayanum	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28969	Solanum sarrachoides	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6890	Euphorbia jolkinii	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18019	Dalbergia oliveri	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12348	Chrysosplenium grayanum	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28969	Solanum sarrachoides	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29519	Primula glaucescens	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16603	Mundulea sericea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29462	Helinus ovatus	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28803	Artocarpus chama	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29358	Senecio oxyodon	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29409	Oenothera laciniata	Species	Onagraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17091	Berberis chilensis	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29318	Cereus validus	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15941	Bacillus licheniformis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO6890	Euphorbia jolkinii	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6876	Ixora coccinea	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29386	Agabus bipustulatus	Species	Dytiscidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17021	Mahonia aquifolia	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO29156	Conyza incana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12348	Chrysosplenium grayanum	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18019	Dalbergia oliveri	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17471	Penicillium obscurum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28969	Solanum sarrachoides	Species	Solanaceae	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 NPC44720 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	478
0.1-0.2	1967
0.2-0.3	4268
0.3-0.4	11029
0.4-0.5	7172
0.5-0.6	3825
0.6-0.7	5379
0.7-0.8	5402
0.8-0.85	2098
0.85-0.9	912
0.9-0.95	150
0.95-1	17

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 NPC44720 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	419
0.1-0.2	1009
0.2-0.3	1741
0.3-0.4	2819
0.4-0.5	1774
0.5-0.6	891
0.6-0.7	340
0.7-0.8	127
0.8-0.85	22
0.85-0.9	8
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