NPASS Compound

Structure

NPC68425 OpenBabel06302216182D 35 38 0 0 1 0 0 0 0 0999 V2000 -0.7812 -5.5909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1731 -5.4907 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5635 -4.6142 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0004 -3.8379 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 -2.8783 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8578 -3.3732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8313 -2.3986 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8312 -1.4392 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0001 -0.9593 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8309 -1.4394 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0264 -1.9347 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6616 -0.9595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4926 -1.4396 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4925 -2.3990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6614 -2.8785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8308 -2.3988 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6617 -0.0002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3618 0.6998 0.0000 O 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 -1.6621 -2.8782 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2260 -2.1021 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1801 -2.2023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7439 -1.4261 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5703 -3.0787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5244 -3.1789 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9146 -4.0553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8687 -4.1555 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4326 -3.3793 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0423 -2.5029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0882 -2.4027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7370 -6.2671 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3466 -7.1436 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6076 -7.2438 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9105 -7.9199 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5202 -8.7965 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 0 0 0 2 3 1 0 0 0 0 2 31 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 16 1 0 0 0 0 5 6 1 6 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 20 1 6 0 0 0 9 8 1 6 0 0 0 9 10 1 0 0 0 0 9 19 1 0 0 0 0 10 16 1 0 0 0 0 10 11 1 6 0 0 0 10 12 1 0 0 0 0 12 13 2 0 0 0 0 12 17 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 16 15 1 6 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 24 1 0 0 0 0 24 25 1 0 0 0 0 25 30 2 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 29 30 1 0 0 0 0 31 32 1 0 0 0 0 32 33 2 0 0 0 0 32 34 1 0 0 0 0 34 35 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	482.27
Volume:	510.2
LogP:	4.713
LogD:	4.514
LogS:	-5.489
# Rotatable Bonds:	11
TPSA:	78.9
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.362
Synthetic Accessibility Score:	4.557
Fsp3:	0.621
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:	-4.87
MDCK Permeability:	4.6957786253187805e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.92
30% Bioavailability (F30%):	0.9

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.058
Plasma Protein Binding (PPB):	96.85214233398438%
Volume Distribution (VD):	0.384
Pgp-substrate:	2.909775972366333%

ADMET: Metabolism

CYP1A2-inhibitor:	0.126
CYP1A2-substrate:	0.106
CYP2C19-inhibitor:	0.817
CYP2C19-substrate:	0.336
CYP2C9-inhibitor:	0.922
CYP2C9-substrate:	0.47
CYP2D6-inhibitor:	0.045
CYP2D6-substrate:	0.174
CYP3A4-inhibitor:	0.913
CYP3A4-substrate:	0.659

ADMET: Excretion

Clearance (CL):	9.005
Half-life (T1/2):	0.737

ADMET: Toxicity

hERG Blockers:	0.226
Human Hepatotoxicity (H-HT):	0.331
Drug-inuced Liver Injury (DILI):	0.314
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.021
Maximum Recommended Daily Dose:	0.939
Skin Sensitization:	0.972
Carcinogencity:	0.052
Eye Corrosion:	0.015
Eye Irritation:	0.452
Respiratory Toxicity:	0.648

Download Data

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

Natural Product: NPC68425

Natural Product ID:	NPC68425
*Common Name:**	YWDQSLLBRGADIX-NFGIMHRHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YWDQSLLBRGADIX-NFGIMHRHSA-N
Standard InCHI:	InChI=1S/C29H38O6/c1-19(15-25(30)33-4)13-14-28(2)21(18-34-26(31)16-20-9-6-5-7-10-20)17-24-29(3)22(27(32)35-24)11-8-12-23(28)29/h5-7,9-11,19,21,23-24H,8,12-18H2,1-4H3/t19-,21+,23-,24+,28+,29+/m1/s1
SMILES:	C[C@H](CC[C@@]1(C)[C@@H](C[C@H]2[C@@]3(C)C(=CCC[C@H]13)C(=O)O2)COC(=O)Cc1ccccc1)CC(=O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0001986] Tricarboxylic acids 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
NPO15810	Zea mays	Species	Poaceae	Eukaryota		n.a.	n.a.	DOI[10.1021/jf00055a023]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	n.a.	seed	n.a.	PMID[11539687]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12713418]
NPO16277	Swertia davidi	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15234768]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21080643]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	n.a.	husk	n.a.	PMID[21574561]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21574561]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	n.a.	seed	n.a.	PMID[23292602]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29762032]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	n.a.	pollen	n.a.	PMID[8987503]
NPO15810	Zea mays	Species	Poaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	Cob	n.a.	n.a.	Database[FooDB]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	Husk Essent. Oil	n.a.	n.a.	Database[FooDB]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	Oil	n.a.	n.a.	Database[FooDB]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	Pollen Or Spore	n.a.	n.a.	Database[FooDB]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	Seed Essent. Oil	n.a.	n.a.	Database[FooDB]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	Silk Essent. Oil	n.a.	n.a.	Database[FooDB]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	Silk Stigma Style	n.a.	n.a.	Database[FooDB]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	Stem	n.a.	n.a.	Database[FooDB]
NPO7730	Commiphora myrrha	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7730	Commiphora myrrha	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8676	Anamirta cocculus	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9657	Melilotus altissima	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21792	Penicillium brefeldianum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7730	Commiphora myrrha	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16277	Swertia davidi	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8676	Anamirta cocculus	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15810	Zea mays	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10380	Prunus triflora	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13904	Jacaranda racemosa	Species	Bignoniaceae	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 NPC68425 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	240
0.1-0.2	1102
0.2-0.3	1851
0.3-0.4	4627
0.4-0.5	9044
0.5-0.6	18029
0.6-0.7	6601
0.7-0.8	1064
0.8-0.85	127
0.85-0.9	12
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 NPC68425 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	205
0.1-0.2	770
0.2-0.3	1134
0.3-0.4	2777
0.4-0.5	2425
0.5-0.6	1396
0.6-0.7	409
0.7-0.8	32
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