NPASS Compound

Structure

NPC110467 OpenBabel06302215402D 35 36 0 0 1 0 0 0 0 0999 V2000 3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1962 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.0622 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5622 -3.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5622 -3.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 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 3.4641 1.0000 0.0000 O 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 3 4 1 0 0 0 0 3 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 6 0 0 0 8 17 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 10 16 1 6 0 0 0 11 12 1 0 0 0 0 11 13 1 0 0 0 0 11 14 1 0 0 0 0 14 15 1 0 0 0 0 17 18 2 0 0 0 0 19 17 1 1 0 0 0 19 20 1 0 0 0 0 19 26 1 0 0 0 0 20 21 1 0 0 0 0 20 35 1 6 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 23 34 1 0 0 0 0 23 24 1 6 0 0 0 23 25 1 0 0 0 0 25 26 1 0 0 0 0 25 34 1 1 0 0 0 26 27 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 30 31 2 0 0 0 0 30 33 1 0 0 0 0 31 32 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	494.25
Volume:	504.432
LogP:	2.286
LogD:	1.016
LogS:	-3.465
# Rotatable Bonds:	12
TPSA:	128.73
# H-Bond Aceptor:	9
# H-Bond Donor:	1
# Rings:	2
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.211
Synthetic Accessibility Score:	5.352
Fsp3:	0.692
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.821
MDCK Permeability:	2.0830300854868256e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.005
Human Intestinal Absorption (HIA):	0.064
20% Bioavailability (F20%):	0.047
30% Bioavailability (F30%):	0.989

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.099
Plasma Protein Binding (PPB):	65.43252563476562%
Volume Distribution (VD):	2.087
Pgp-substrate:	9.537729263305664%

ADMET: Metabolism

CYP1A2-inhibitor:	0.015
CYP1A2-substrate:	0.266
CYP2C19-inhibitor:	0.27
CYP2C19-substrate:	0.875
CYP2C9-inhibitor:	0.554
CYP2C9-substrate:	0.042
CYP2D6-inhibitor:	0.015
CYP2D6-substrate:	0.083
CYP3A4-inhibitor:	0.895
CYP3A4-substrate:	0.658

ADMET: Excretion

Clearance (CL):	8.899
Half-life (T1/2):	0.577

ADMET: Toxicity

hERG Blockers:	0.024
Human Hepatotoxicity (H-HT):	0.684
Drug-inuced Liver Injury (DILI):	0.437
AMES Toxicity:	0.024
Rat Oral Acute Toxicity:	0.413
Maximum Recommended Daily Dose:	0.494
Skin Sensitization:	0.174
Carcinogencity:	0.039
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.278

Download Data

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

Natural Product: NPC110467

Natural Product ID:	NPC110467
*Common Name:**	DHYQZUBULNBFRY-APRVYDDCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DHYQZUBULNBFRY-APRVYDDCSA-N
Standard InCHI:	InChI=1S/C26H38O9/c1-10-13(3)23(30)33-16(12-17(27)25(6,7)32-9)15(5)18-19(28)21(29)26(8)22(35-26)20(18)34-24(31)14(4)11-2/h10-11,16-20,22,27-28H,5,12H2,1-4,6-9H3/b13-10-,14-11-/t16-,17-,18-,19-,20+,22-,26+/m1/s1
SMILES:	C/C=C(/C)C(=O)O[C@H](C[C@H](C(C)(C)OC)O)C(=C)[C@@H]1[C@H](C(=O)[C@@]2(C)[C@@H]([C@H]1OC(=O)/C(=CC)/C)O2)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:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids

*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
NPO1315	Sinomenium acutum	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.3987/COM-96-7609.]
NPO403	Gentiana lutea	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10705751]
NPO403	Gentiana lutea	Species	Gentianaceae	Eukaryota	n.a.	seed	n.a.	PMID[12822897]
NPO1315	Sinomenium acutum	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16038566]
NPO1315	Sinomenium acutum	Species	Menispermaceae	Eukaryota	n.a.	stem	n.a.	PMID[16964757]
NPO403	Gentiana lutea	Species	Gentianaceae	Eukaryota	n.a.	root	n.a.	PMID[18064621]
NPO403	Gentiana lutea	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18064621]
NPO1315	Sinomenium acutum	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18081254]
NPO1315	Sinomenium acutum	Species	Menispermaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[23059629]
NPO403	Gentiana lutea	Species	Gentianaceae	Eukaryota	n.a.	root	n.a.	PMID[24257774]
NPO1451	Aspergillus duricaulis	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26517152]
NPO1315	Sinomenium acutum	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO403	Gentiana lutea	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1315	Sinomenium acutum	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO403	Gentiana lutea	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO403	Gentiana lutea	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1315	Sinomenium acutum	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO403	Gentiana lutea	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1315	Sinomenium acutum	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1380	Phylica rogersii	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1451	Aspergillus duricaulis	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO403	Gentiana lutea	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18088	Euglena longa	Species	Euglenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7529	Viscum multinerve	Species	Viscaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3817	Chrysosporium queenslandicum	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4851	Penstemon confertus	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4484	Maytenus obtusifolia	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1315	Sinomenium acutum	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3315	Eucalyptus hybr	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2343	Haplopappus arbutoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3691	Albizia mollis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10901	Tessaria dodoneaefolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4944	Bactris plumeriana	Species	Arecaceae	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 NPC110467 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	258
0.1-0.2	1743
0.2-0.3	4684
0.3-0.4	7517
0.4-0.5	13495
0.5-0.6	9705
0.6-0.7	4196
0.7-0.8	989
0.8-0.85	79
0.85-0.9	27
0.9-0.95	3
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 NPC110467 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	260
0.1-0.2	2254
0.2-0.3	3498
0.3-0.4	1982
0.4-0.5	775
0.5-0.6	278
0.6-0.7	92
0.7-0.8	11
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