NPASS Compound

Structure

NPC298676 OpenBabel06302215512D 59 61 0 0 1 0 0 0 0 0999 V2000 -5.4920 1.6290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0504 0.7876 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5583 -0.0155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5822 0.5780 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.3276 1.1146 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8527 1.4714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2252 2.3456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2665 1.5667 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.7031 1.3786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2916 0.9502 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.1264 0.3797 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2452 -0.2023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6208 -0.6623 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.1673 -0.8952 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.6594 -0.0920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1010 0.7493 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5931 1.5524 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6437 1.5142 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2021 0.6728 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1358 2.3173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1167 -0.8569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1550 -1.8063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9581 -1.2985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0500 -1.4220 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4224 -2.2961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8516 -3.0558 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3657 -2.4107 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9848 0.7870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0613 1.7342 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4973 2.8137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5737 3.7609 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6388 2.4064 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6458 1.9004 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8229 1.4253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8229 0.4751 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.9004 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8229 1.4253 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8229 0.4751 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6458 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6458 -0.9502 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8229 -1.4253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.9502 0.0000 C 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 1.6458 1.9004 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.4687 1.4253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6458 2.8506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.8506 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1900 2.5138 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9720 3.0536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8305 2.6462 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8955 4.0007 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7996 2.3165 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6881 1.9795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8405 1.0416 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.4241 2.5805 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5132 0.7680 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.1433 0.0568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8424 -0.8445 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.0743 0.2468 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 16 1 0 0 0 0 2 3 2 0 0 0 0 3 21 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 4 56 1 1 0 0 0 5 6 2 0 0 0 0 5 52 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 8 48 1 1 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 10 33 1 6 0 0 0 11 12 2 0 0 0 0 11 28 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 13 24 1 6 0 0 0 14 15 1 6 0 0 0 14 21 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 1 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 18 20 1 0 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 25 27 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 30 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 36 37 1 0 0 0 0 36 47 1 6 0 0 0 37 38 1 0 0 0 0 37 44 1 1 0 0 0 38 43 2 0 0 0 0 38 39 1 0 0 0 0 39 40 2 0 0 0 0 40 41 1 0 0 0 0 41 42 2 0 0 0 0 42 43 1 0 0 0 0 44 45 1 0 0 0 0 44 46 1 0 0 0 0 48 49 1 0 0 0 0 49 50 2 0 0 0 0 49 51 1 0 0 0 0 52 53 1 0 0 0 0 53 54 2 0 0 0 0 53 55 1 0 0 0 0 56 57 1 0 0 0 0 57 58 2 0 0 0 0 57 59 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	827.37
Volume:	835.191
LogP:	3.527
LogD:	2.386
LogS:	-3.725
# Rotatable Bonds:	19
TPSA:	207.57
# H-Bond Aceptor:	16
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	16

MedChem Properties

QED Drug-Likeness Score:	0.176
Synthetic Accessibility Score:	6.608
Fsp3:	0.558
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:	-5.322
MDCK Permeability:	0.0004606950387824327
Pgp-inhibitor:	1.0
Pgp-substrate:	1.0
Human Intestinal Absorption (HIA):	0.596
20% Bioavailability (F20%):	0.573
30% Bioavailability (F30%):	0.969

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.023
Plasma Protein Binding (PPB):	77.46461486816406%
Volume Distribution (VD):	1.221
Pgp-substrate:	19.237394332885742%

ADMET: Metabolism

CYP1A2-inhibitor:	0.008
CYP1A2-substrate:	0.009
CYP2C19-inhibitor:	0.024
CYP2C19-substrate:	0.12
CYP2C9-inhibitor:	0.196
CYP2C9-substrate:	0.039
CYP2D6-inhibitor:	0.063
CYP2D6-substrate:	0.072
CYP3A4-inhibitor:	0.352
CYP3A4-substrate:	0.763

ADMET: Excretion

Clearance (CL):	3.572
Half-life (T1/2):	0.012

ADMET: Toxicity

hERG Blockers:	0.263
Human Hepatotoxicity (H-HT):	0.995
Drug-inuced Liver Injury (DILI):	0.984
AMES Toxicity:	0.065
Rat Oral Acute Toxicity:	0.937
Maximum Recommended Daily Dose:	0.985
Skin Sensitization:	0.343
Carcinogencity:	0.025
Eye Corrosion:	0.003
Eye Irritation:	0.011
Respiratory Toxicity:	0.979

Download Data

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

Natural Product: NPC298676

Natural Product ID:	NPC298676
*Common Name:**	HECZDVAZGHHUKK-ZABKVODASA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HECZDVAZGHHUKK-ZABKVODASA-N
Standard InCHI:	InChI=1S/C43H57NO15/c1-22-33(54-25(4)46)19-32-36(56-27(6)48)18-31(21-53-24(3)45)35(59-42(52)39(51)38(44(11)12)30-16-14-13-15-17-30)20-34(55-26(5)47)23(2)40(57-28(7)49)41(58-29(8)50)37(22)43(32,9)10/h13-18,32-36,38-39,41,51H,19-21H2,1-12H3/b31-18+,40-23+/t32-,33-,34-,35-,36-,38-,39+,41+/m0/s1
SMILES:	CC1=C2[C@H](/C(=C(/C)[C@H](C[C@@H](/C(=C/[C@@H]([C@H](C[C@@H]1OC(=O)C)C2(C)C)OC(=O)C)/COC(=O)C)OC(=O)[C@@H]([C@H](c1ccccc1)N(C)C)O)OC(=O)C)/OC(=O)C)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	100931295
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0000676] Taxanes and derivatives

*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
NPO11132	Alangium longiflorum	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30106296]
NPO10084	Equisetum hyemale	Species	Equisetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15125.1	Taxus wallichiana var. chinensis	Varieties	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27451	Ophiocordyceps sinensis	Species	Ophiocordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10084	Equisetum hyemale	Species	Equisetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO27451	Ophiocordyceps sinensis	Species	Ophiocordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO27451	Ophiocordyceps sinensis	Species	Ophiocordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10953	Papaver strigosum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15125.1	Taxus wallichiana var. chinensis	Varieties	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22296	Rheum tataricum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10084	Equisetum hyemale	Species	Equisetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11819	Trichophyton megnini	Species	Arthrodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7785	Boletus fomentarius	Species	Boletaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12272	Calceolaria petiolaris	Species	Calceolariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21703	Maianthemum atropurpureum	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12615	Athrotaxis selaginoides	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11936	Ptilocaulis walpersi	Species	Axinellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3362	Dictyostelium mucoroides	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO563	Leucopaxillus cerealis	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11132	Alangium longiflorum	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10487	Rosa americana	Species	Rosaceae	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 NPC298676 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	170
0.1-0.2	649
0.2-0.3	1886
0.3-0.4	5817
0.4-0.5	15408
0.5-0.6	16516
0.6-0.7	2172
0.7-0.8	75
0.8-0.85	3
0.85-0.9	1
0.9-0.95	0
0.95-1	0

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 NPC298676 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	124
0.1-0.2	390
0.2-0.3	863
0.3-0.4	1991
0.4-0.5	3012
0.5-0.6	2214
0.6-0.7	493
0.7-0.8	63
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