NPASS Compound

Structure

NPC135076 OpenBabel06302215272D 40 44 0 0 1 0 0 0 0 0999 V2000 -0.0000 1.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1691 -1.6092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0827 -1.2024 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0827 -2.2024 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.2167 -2.7024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9487 -2.7024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8147 -2.2024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8147 -1.2024 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.6808 -0.7024 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.6808 -1.7024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5468 -1.2024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4128 -0.7024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4128 0.2976 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.5468 0.7976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0468 1.6636 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0468 1.6636 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6808 0.2976 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.8147 0.7976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9487 0.2976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9487 -0.7024 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.0827 -0.2024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2788 0.7976 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.1449 0.2976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0109 0.7976 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.1449 -0.7024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9781 -0.2079 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 2.0000 -1.7321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0000 -1.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5000 -2.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5000 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5000 0.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0000 1.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 32 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 4 37 1 0 0 0 0 5 6 2 0 0 0 0 5 33 1 0 0 0 0 6 32 1 0 0 0 0 6 7 1 0 0 0 0 8 7 1 6 0 0 0 8 25 1 0 0 0 0 8 9 1 0 0 0 0 8 31 1 0 0 0 0 9 10 1 1 0 0 0 9 11 1 0 0 0 0 11 12 1 0 0 0 0 13 12 1 6 0 0 0 13 14 1 0 0 0 0 13 25 1 0 0 0 0 14 22 1 0 0 0 0 14 15 1 6 0 0 0 14 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 18 27 1 6 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 19 22 1 0 0 0 0 22 23 1 6 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 6 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 28 30 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 36 1 0 0 0 0 37 38 1 0 0 0 0 38 39 2 0 0 0 0 38 40 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	554.32
Volume:	582.255
LogP:	6.29
LogD:	4.263
LogS:	-5.278
# Rotatable Bonds:	6
TPSA:	88.13
# H-Bond Aceptor:	7
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.302
Synthetic Accessibility Score:	5.116
Fsp3:	0.727
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:	-5.071
MDCK Permeability:	1.3709437553188764e-05
Pgp-inhibitor:	0.998
Pgp-substrate:	0.008
Human Intestinal Absorption (HIA):	0.022
20% Bioavailability (F20%):	0.118
30% Bioavailability (F30%):	0.922

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.558
Plasma Protein Binding (PPB):	90.6938247680664%
Volume Distribution (VD):	0.866
Pgp-substrate:	11.0369873046875%

ADMET: Metabolism

CYP1A2-inhibitor:	0.055
CYP1A2-substrate:	0.081
CYP2C19-inhibitor:	0.084
CYP2C19-substrate:	0.856
CYP2C9-inhibitor:	0.294
CYP2C9-substrate:	0.495
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.459
CYP3A4-inhibitor:	0.435
CYP3A4-substrate:	0.564

ADMET: Excretion

Clearance (CL):	2.765
Half-life (T1/2):	0.101

ADMET: Toxicity

hERG Blockers:	0.009
Human Hepatotoxicity (H-HT):	0.02
Drug-inuced Liver Injury (DILI):	0.51
AMES Toxicity:	0.004
Rat Oral Acute Toxicity:	0.59
Maximum Recommended Daily Dose:	0.536
Skin Sensitization:	0.817
Carcinogencity:	0.041
Eye Corrosion:	0.003
Eye Irritation:	0.106
Respiratory Toxicity:	0.918

Download Data

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

Natural Product: NPC135076

Natural Product ID:	NPC135076
*Common Name:**	QYWYPTRFMCEXQU-XGNZJLIISA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QYWYPTRFMCEXQU-XGNZJLIISA-N
Standard InCHI:	InChI=1S/C33H46O7/c1-18-16-24(37-20(3)34)29(39-22(5)36)23-17-33(40-28(18)23)19(2)10-11-26-31(8)14-13-27(38-21(4)35)30(6,7)25(31)12-15-32(26,33)9/h16,19,25-27H,10-15,17H2,1-9H3/t19-,25-,26+,27-,31-,32+,33-/m0/s1
SMILES:	Cc1cc(c(c2C[C@@]3([C@@H](C)CC[C@@H]4[C@@]5(C)CC[C@@H](C(C)(C)[C@@H]5CC[C@@]34C)OC(=O)C)Oc12)OC(=O)C)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10460325
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0002550] Isocopalane and spongiane diterpenoids

*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
NPO21080	Solanum lycopersicum	Species	Solanaceae	Eukaryota	n.a.	fruit	n.a.	DOI[10.1007/s11306-014-0728-9]
NPO21080	Solanum lycopersicum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1038/sdata.2014.29]
NPO19009	Ipomoea orizabensis	Species	Convolvulaceae	Eukaryota	Roots	Mexican	n.a.	PMID[10479311]
NPO21080	Solanum lycopersicum	Species	Solanaceae	Eukaryota	n.a.	fruit	n.a.	PMID[11171227]
NPO21080	Solanum lycopersicum	Species	Solanaceae	Eukaryota	n.a.	fruit	n.a.	PMID[12576668]
NPO19009	Ipomoea orizabensis	Species	Convolvulaceae	Eukaryota	crude resin	Mexican	n.a.	PMID[16562846]
NPO14026.1	Vitex negundo var. cannabifolia	Varieties	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25245917]
NPO21080	Solanum lycopersicum	Species	Solanaceae	Eukaryota	n.a.	seed	n.a.	PMID[25891114]
NPO21080	Solanum lycopersicum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8987503]
NPO21485	Polygala sibirica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21080	Solanum lycopersicum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO21080	Solanum lycopersicum	Species	Solanaceae	Eukaryota	n.a.	fruit	n.a.	Database[MetaboLights]
NPO21485	Polygala sibirica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18614	Gentiana turkestanorum	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21080	Solanum lycopersicum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21485	Polygala sibirica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21485	Polygala sibirica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4243	Didymocarpus leucocalyx	Species	Gesneriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14026.1	Vitex negundo var. cannabifolia	Varieties	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20473	Vaccinium membranaceum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21485	Polygala sibirica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16442	Omphalia campanella	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO19009	Ipomoea orizabensis	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18614	Gentiana turkestanorum	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19772	Ceroplastes ceriferus	Species	Coccidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21080	Solanum lycopersicum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20669	Baccharis rhetinodes	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21549	Consolida raveyi	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14033	Torilis arvensis	Species	Apiaceae	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 NPC135076 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	460
0.1-0.2	1689
0.2-0.3	3725
0.3-0.4	8421
0.4-0.5	9917
0.5-0.6	5645
0.6-0.7	9530
0.7-0.8	3227
0.8-0.85	76
0.85-0.9	6
0.9-0.95	0
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 NPC135076 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	356
0.1-0.2	952
0.2-0.3	1954
0.3-0.4	2752
0.4-0.5	1774
0.5-0.6	867
0.6-0.7	436
0.7-0.8	59
0.8-0.85	0
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