NPASS Compound

Structure

NPC61530 OpenBabel06302216132D 40 43 0 0 1 0 0 0 0 0999 V2000 -1.6925 -4.8934 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8452 -4.4039 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8455 -3.4254 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0023 -4.8929 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8496 -4.4035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8280 -4.4032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3390 -5.2507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8493 -3.4250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0017 -2.9360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0015 -1.9575 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8461 -1.4685 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8487 -1.4680 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8272 -1.4677 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8484 -0.4895 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.6954 0.0005 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6951 0.9794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 0.9789 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0006 1.9789 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8487 1.4684 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.8490 2.4479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6974 2.9374 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5456 2.4474 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5453 1.4679 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -3.3929 0.9779 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2407 1.4674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2410 2.4469 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1072 2.9465 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3934 2.9369 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3937 3.9369 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2594 3.4369 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1067 0.9673 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 -1.6969 0.9784 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5628 0.4782 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6966 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5625 -0.5007 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8482 -0.4900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0003 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5617 -0.4990 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3382 -2.3152 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 2 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 5 8 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 12 13 1 6 0 0 0 12 14 1 0 0 0 0 12 40 1 0 0 0 0 14 37 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 39 1 1 0 0 0 16 17 1 0 0 0 0 17 37 1 0 0 0 0 17 18 1 1 0 0 0 17 19 1 0 0 0 0 19 32 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 22 28 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 23 32 1 0 0 0 0 24 25 2 0 0 0 0 25 26 1 0 0 0 0 25 31 1 0 0 0 0 26 27 2 0 0 0 0 26 28 1 0 0 0 0 28 29 1 0 0 0 0 28 30 1 0 0 0 0 32 33 1 6 0 0 0 32 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 37 38 1 6 0 0 0 M CHG 1 31 -1 M END $$$$

Physi-Chem Properties

Molecular Weight:	556.3
Volume:	579.669
LogP:	2.58
LogD:	2.233
LogS:	-4.553
# Rotatable Bonds:	6
TPSA:	135.04
# H-Bond Aceptor:	8
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.227
Synthetic Accessibility Score:	5.563
Fsp3:	0.719
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.155
MDCK Permeability:	2.4663382646394894e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.671
20% Bioavailability (F20%):	0.602
30% Bioavailability (F30%):	0.304

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.981
Plasma Protein Binding (PPB):	71.42385864257812%
Volume Distribution (VD):	0.445
Pgp-substrate:	22.943653106689453%

ADMET: Metabolism

CYP1A2-inhibitor:	0.004
CYP1A2-substrate:	0.549
CYP2C19-inhibitor:	0.093
CYP2C19-substrate:	0.79
CYP2C9-inhibitor:	0.092
CYP2C9-substrate:	0.133
CYP2D6-inhibitor:	0.026
CYP2D6-substrate:	0.067
CYP3A4-inhibitor:	0.859
CYP3A4-substrate:	0.796

ADMET: Excretion

Clearance (CL):	2.483
Half-life (T1/2):	0.068

ADMET: Toxicity

hERG Blockers:	0.007
Human Hepatotoxicity (H-HT):	0.169
Drug-inuced Liver Injury (DILI):	0.215
AMES Toxicity:	0.029
Rat Oral Acute Toxicity:	0.24
Maximum Recommended Daily Dose:	0.539
Skin Sensitization:	0.125
Carcinogencity:	0.659
Eye Corrosion:	0.003
Eye Irritation:	0.01
Respiratory Toxicity:	0.537

Download Data

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

Natural Product: NPC61530

Natural Product ID:	NPC61530
*Common Name:**	NDYMQXYDSVBNLL-GPIPDBLZSA-M
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NDYMQXYDSVBNLL-GPIPDBLZSA-M
Standard InCHI:	InChI=1S/C32H44O8/c1-17(33)40-27(2,3)13-12-23(36)32(9,39)25-21(35)15-29(6)22-11-10-18-19(14-20(34)26(38)28(18,4)5)31(22,8)24(37)16-30(25,29)7/h10,12-14,19,21-22,25,34-35,39H,11,15-16H2,1-9H3/p-1/b13-12+/t19?,21-,22?,25?,29+,30-,31+,32+/m1/s1
SMILES:	CC(=O)OC(C)(C)/C=C/C(=O)[C@@](C)(C1[C@@H](C[C@@]2(C)C3CC=C4C(C=C(C(=O)C4(C)C)[O-])[C@]3(C)C(=O)C[C@]12C)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	25245182
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001686] Cucurbitacins

*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
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jfca.2004.07.004]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jfca.2005.08.001]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12379786]
NPO24454	Begonia nantoensis	Species	Begoniaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[14993759]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18460139]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota	Stems	n.a.	n.a.	PMID[19348465]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23507362]
NPO14558	Aquilaria sinensis	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27128895]
NPO14558	Aquilaria sinensis	Species	Thymelaeaceae	Eukaryota	Resinous Wood	n.a.	n.a.	PMID[29227647]
NPO11699	Ecballium elaterium	Species	Cucurbitaceae	Eukaryota	Fruit juice	n.a.	n.a.	PMID[3404148]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	Cotyledon	n.a.	n.a.	Database[FooDB]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota	Cotyledon	n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	Seed Oil	n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO11699	Ecballium elaterium	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3344	Bryonia alba	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13846	Crinodendron hookerianum	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14558	Aquilaria sinensis	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24454	Begonia nantoensis	Species	Begoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24328	Gratiola officinalis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11699	Ecballium elaterium	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14558	Aquilaria sinensis	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13846	Crinodendron hookerianum	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3344	Bryonia alba	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8111	Rhizoma bolbostemmae	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24454	Begonia nantoensis	Species	Begoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24328	Gratiola officinalis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14558	Aquilaria sinensis	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14558	Aquilaria sinensis	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3344	Bryonia alba	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11699	Ecballium elaterium	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24454	Begonia nantoensis	Species	Begoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24328	Gratiola officinalis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13846	Crinodendron hookerianum	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14558	Aquilaria sinensis	Species	Thymelaeaceae	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 NPC61530 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	199
0.1-0.2	1175
0.2-0.3	4084
0.3-0.4	8349
0.4-0.5	13012
0.5-0.6	7068
0.6-0.7	6422
0.7-0.8	2173
0.8-0.85	177
0.85-0.9	27
0.9-0.95	10
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 NPC61530 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	174
0.1-0.2	1408
0.2-0.3	3631
0.3-0.4	2562
0.4-0.5	840
0.5-0.6	230
0.6-0.7	146
0.7-0.8	126
0.8-0.85	33
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