NPASS Compound

Structure

NPC206161 OpenBabel06302215102D 35 40 0 0 1 0 0 0 0 0999 V2000 -0.8334 1.4118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 0.9305 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8337 0.4497 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8065 1.3961 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8068 2.3276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6137 2.7931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6139 3.7553 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4197 2.3274 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4203 4.2518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4194 1.3959 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.2260 0.9299 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0328 1.3955 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0331 2.3270 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.8662 1.8456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8396 2.7920 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.6458 2.3263 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4964 2.7047 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1192 2.0127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6534 1.2065 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7428 1.4003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8396 3.7230 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0331 4.1890 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0335 5.1455 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2265 3.7239 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.2265 2.7929 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4203 3.2584 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6126 0.9304 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8061 -0.4657 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 3.2247 -0.0010 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.1271 -0.9268 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8801 -1.4742 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7825 -2.3999 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7306 -1.0958 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0752 0.3774 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 29 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 1 0 0 0 4 27 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 8 1 0 0 0 0 8 25 1 0 0 0 0 8 9 1 6 0 0 0 8 10 1 0 0 0 0 10 11 1 6 0 0 0 10 27 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 25 1 0 0 0 0 13 14 1 1 0 0 0 13 15 1 0 0 0 0 15 16 1 1 0 0 0 15 21 1 0 0 0 0 16 20 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 24 22 1 6 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 25 26 1 6 0 0 0 27 28 1 0 0 0 0 27 30 1 1 0 0 0 28 29 1 0 0 0 0 30 31 1 0 0 0 0 30 35 1 6 0 0 0 31 32 1 0 0 0 0 32 33 2 0 0 0 0 32 34 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	488.2
Volume:	472.843
LogP:	1.211
LogD:	0.634
LogS:	-4.431
# Rotatable Bonds:	4
TPSA:	135.8
# H-Bond Aceptor:	9
# H-Bond Donor:	2
# Rings:	6
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.484
Synthetic Accessibility Score:	5.873
Fsp3:	0.731
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.522
MDCK Permeability:	1.617398447706364e-05
Pgp-inhibitor:	0.023
Pgp-substrate:	0.024
Human Intestinal Absorption (HIA):	0.016
20% Bioavailability (F20%):	0.891
30% Bioavailability (F30%):	0.96

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.785
Plasma Protein Binding (PPB):	67.96282196044922%
Volume Distribution (VD):	0.323
Pgp-substrate:	31.100406646728516%

ADMET: Metabolism

CYP1A2-inhibitor:	0.004
CYP1A2-substrate:	0.108
CYP2C19-inhibitor:	0.014
CYP2C19-substrate:	0.525
CYP2C9-inhibitor:	0.024
CYP2C9-substrate:	0.052
CYP2D6-inhibitor:	0.02
CYP2D6-substrate:	0.136
CYP3A4-inhibitor:	0.05
CYP3A4-substrate:	0.205

ADMET: Excretion

Clearance (CL):	6.246
Half-life (T1/2):	0.885

ADMET: Toxicity

hERG Blockers:	0.029
Human Hepatotoxicity (H-HT):	0.328
Drug-inuced Liver Injury (DILI):	0.897
AMES Toxicity:	0.283
Rat Oral Acute Toxicity:	0.982
Maximum Recommended Daily Dose:	0.96
Skin Sensitization:	0.226
Carcinogencity:	0.498
Eye Corrosion:	0.004
Eye Irritation:	0.049
Respiratory Toxicity:	0.961

Download Data

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

Natural Product: NPC206161

Natural Product ID:	NPC206161
*Common Name:**	SZSLZBYOLTYIOE-RZUFXSGTSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SZSLZBYOLTYIOE-RZUFXSGTSA-N
Standard InCHI:	InChI=1S/C26H32O9/c1-22(2)15-9-16(27)24(4)14(25(15,12-33-22)17(28)10-18(29)30)5-7-23(3)19(13-6-8-32-11-13)34-21(31)20-26(23,24)35-20/h6,8,11,14-15,17,19-20,28H,5,7,9-10,12H2,1-4H3,(H,29,30)/t14-,15+,17+,19-,20+,23-,24-,25+,26+/m0/s1
SMILES:	CC1(C)[C@H]2CC(=O)[C@]3(C)[C@H](CC[C@@]4(C)[C@H](c5ccoc5)OC(=O)[C@@H]5[C@]34O5)[C@@]2(CO1)[C@@H](CC(=O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001125] Steroid lactones

*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
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12628396]
NPO2236	Pyrola rotundifolia	Species	Ericaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[16079548]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	Hairy roots	n.a.	n.a.	PMID[19271765]
NPO5489	Cinnamomum tenuifolium	Species	Lauraceae	Eukaryota	stems	n.a.	n.a.	PMID[19754130]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota	n.a.	leaf	n.a.	PMID[24024688]
NPO8528	Citrus junos	Species	Rutaceae	Eukaryota	n.a.	fruit	n.a.	PMID[25522543]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26285573]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6619887]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6631435]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7264679]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7264682]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7320741]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7798960]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2236	Pyrola rotundifolia	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8528	Citrus junos	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2236	Pyrola rotundifolia	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8528	Citrus junos	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11107	Stevia alpina	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7263	Phyllobates aurotaenia	Species	Dendrobatidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5489	Cinnamomum tenuifolium	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29494	Stoeba extensa	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO7003	Streptomyces violaceochromogenes	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO8528	Citrus junos	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10402	Strophanthus eminii	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9919	Jaspis stellifera	Species	Ancorinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2236	Pyrola rotundifolia	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17324	Pluchea dioscoridis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9765	Petriella guttulata	Species	Microascaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4311	Asterolasia squamuligera	Species	Rutaceae	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 NPC206161 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	355
0.1-0.2	1397
0.2-0.3	3192
0.3-0.4	5448
0.4-0.5	10618
0.5-0.6	10698
0.6-0.7	9227
0.7-0.8	1304
0.8-0.85	267
0.85-0.9	121
0.9-0.95	61
0.95-1	9

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 NPC206161 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	299
0.1-0.2	974
0.2-0.3	2232
0.3-0.4	2689
0.4-0.5	1866
0.5-0.6	819
0.6-0.7	250
0.7-0.8	19
0.8-0.85	2
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