NPASS Compound

Structure

NPC33894 OpenBabel06302216032D 67 71 0 0 1 0 0 0 0 0999 V2000 -2.9421 -0.3092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5217 0.4886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1207 1.3894 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7003 2.1872 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.6810 2.0841 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0821 1.1833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5025 0.3855 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0628 1.0802 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6424 1.8780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6231 1.7749 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.1162 0.9209 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.7151 0.0200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.0807 1.1259 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.1838 2.1066 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.2830 2.5077 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.0779 3.4723 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.1401 3.7770 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.8108 4.1321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.7486 3.8274 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.0378 2.5997 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.8918 2.1066 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.7458 2.5997 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.8918 0.1344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.7458 -0.3587 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -11.7458 -1.3448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.8918 -1.8378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.0378 -1.3448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.5998 -1.8378 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -13.4538 -1.3448 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -13.4538 -0.3587 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.5998 0.1344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.5998 1.1205 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.7458 1.6136 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -13.4538 1.6136 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -14.3078 1.1205 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.5998 -2.8239 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -13.4538 -3.3170 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -13.4538 -4.3031 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -14.3078 -4.7962 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -15.1618 -4.3031 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -15.1618 -3.3170 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -16.0158 -2.8239 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -16.8698 -3.3170 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -14.3078 -2.8239 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -16.0158 -4.7962 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -14.3078 -5.7823 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -12.5998 -4.7962 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2992 3.0880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3185 3.1911 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7389 2.3933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1400 1.4925 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5603 0.6947 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5796 0.7978 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1785 1.6986 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8022 1.8017 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3818 1.0039 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9807 0.1031 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5603 -0.6947 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5410 -0.5916 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 2.3625 1.1070 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2033 2.7026 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7582 2.4964 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8788 3.8858 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8595 3.7827 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4777 4.7867 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0574 5.5845 0.0000 C 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 51 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 6 0 0 0 4 48 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 10 9 1 6 0 0 0 10 11 1 0 0 0 0 10 15 1 0 0 0 0 11 12 1 1 0 0 0 11 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 20 1 6 0 0 0 15 16 1 1 0 0 0 16 17 1 6 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 24 23 1 1 0 0 0 24 25 1 0 0 0 0 24 31 1 0 0 0 0 25 26 2 0 0 0 0 25 28 1 0 0 0 0 26 27 1 0 0 0 0 28 29 1 0 0 0 0 28 36 1 6 0 0 0 29 30 1 0 0 0 0 30 31 2 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 37 36 1 1 0 0 0 37 38 1 0 0 0 0 37 44 1 0 0 0 0 38 39 1 0 0 0 0 38 47 1 6 0 0 0 39 40 1 0 0 0 0 39 46 1 1 0 0 0 40 41 1 0 0 0 0 40 45 1 6 0 0 0 41 42 1 1 0 0 0 41 44 1 0 0 0 0 42 43 1 0 0 0 0 48 49 2 0 0 0 0 48 64 1 0 0 0 0 49 50 1 0 0 0 0 50 51 1 0 0 0 0 51 52 1 1 0 0 0 53 52 1 1 0 0 0 53 54 1 0 0 0 0 53 60 1 0 0 0 0 54 55 1 0 0 0 0 54 63 1 6 0 0 0 55 56 1 0 0 0 0 55 62 1 1 0 0 0 56 57 1 0 0 0 0 56 61 1 6 0 0 0 57 58 1 1 0 0 0 57 60 1 0 0 0 0 58 59 1 0 0 0 0 64 65 2 0 0 0 0 64 66 1 0 0 0 0 66 67 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	204.19
Volume:	245.61
LogP:	4.527
LogD:	4.406
LogS:	-5.258
# Rotatable Bonds:	2
TPSA:	0.0
# H-Bond Aceptor:	0
# H-Bond Donor:	0
# Rings:	2
# Heavy Atoms:	0

MedChem Properties

QED Drug-Likeness Score:	0.577
Synthetic Accessibility Score:	4.713
Fsp3:	0.733
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.637
MDCK Permeability:	1.8003751392825507e-05
Pgp-inhibitor:	0.255
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.011
20% Bioavailability (F20%):	0.107
30% Bioavailability (F30%):	0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.244
Plasma Protein Binding (PPB):	85.87883758544922%
Volume Distribution (VD):	2.056
Pgp-substrate:	13.483041763305664%

ADMET: Metabolism

CYP1A2-inhibitor:	0.077
CYP1A2-substrate:	0.721
CYP2C19-inhibitor:	0.431
CYP2C19-substrate:	0.947
CYP2C9-inhibitor:	0.264
CYP2C9-substrate:	0.609
CYP2D6-inhibitor:	0.195
CYP2D6-substrate:	0.63
CYP3A4-inhibitor:	0.628
CYP3A4-substrate:	0.482

ADMET: Excretion

Clearance (CL):	6.097
Half-life (T1/2):	0.066

ADMET: Toxicity

hERG Blockers:	0.006
Human Hepatotoxicity (H-HT):	0.05
Drug-inuced Liver Injury (DILI):	0.019
AMES Toxicity:	0.009
Rat Oral Acute Toxicity:	0.059
Maximum Recommended Daily Dose:	0.235
Skin Sensitization:	0.05
Carcinogencity:	0.063
Eye Corrosion:	0.936
Eye Irritation:	0.959
Respiratory Toxicity:	0.908

Download Data

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

Natural Product: NPC33894

Natural Product ID:	NPC33894
*Common Name:**	VCJYHQPAJJKWLH-VMTDYQMDSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VCJYHQPAJJKWLH-VMTDYQMDSA-N
Standard InCHI:	InChI=1S/C44H64O23/c1-7-20-22(25(39(56)58-5)16-61-41(20)66-43-37(54)35(52)33(50)28(13-46)64-43)10-30(48)60-15-24-18(3)9-27(32(24)19(4)12-45)63-31(49)11-23-21(8-2)42(62-17-26(23)40(57)59-6)67-44-38(55)36(53)34(51)29(14-47)65-44/h7-8,16-19,22-24,27-29,32-38,41-47,50-55H,9-15H2,1-6H3/b20-7+,21-8+/t18-,19-,22-,23-,24+,27-,28+,29+,32-,33+,34+,35-,36-,37+,38+,41-,42-,43-,44-/m0/s1
SMILES:	C/C=C/1[C@H](CC(=O)OC[C@@H]2[C@@H](C)C[C@@H]([C@H]2[C@@H](C)CO)OC(=O)C[C@H]2/C(=CC)/[C@@H](OC=C2C(=O)OC)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)C(=CO[C@H]1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)C(=O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10581755
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides

*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
NPO1552	Euonymus japonicus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1039/P19890001079]
NPO12062	Pseudoxandra cuspidata	Species	Annonaceae	Eukaryota	Bark	n.a.	n.a.	PMID[19299148]
NPO8614	Cinchona succirubra	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1552	Euonymus japonicus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1552	Euonymus japonicus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8614	Cinchona succirubra	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1552	Euonymus japonicus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14219	Aconitum racemulosum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15910	Calea morii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12062	Pseudoxandra cuspidata	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1197	Panax trifoliatus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10656	Rzedowskia tolantonguensis	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12298	Epilobium parviflorum	Species	Onagraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6240	Paliurus spina-christi	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8614	Cinchona succirubra	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11272	Plectranthus parviflorus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3128	Solanum dasyphyllum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9574	Trametes albida	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14343	Scapharca broughtonii	Species	Arcidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1552	Euonymus japonicus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16173	Parmelia norcrambidiocarpa	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15096	Penicillium sclerotiorum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10146	Bassia parkii	Species	Abylidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13363	Rumex aquaticus	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13239	Eudistoma toealensis	Species	Polycitoridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15423	Senecio ilicifolius	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11606	Anemoclema glaucifolium	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2891	Montanelia tominii	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14760	Eulophia ochreata	Species	Orchidaceae	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 NPC33894 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	219
0.1-0.2	1330
0.2-0.3	4524
0.3-0.4	9367
0.4-0.5	12371
0.5-0.6	8423
0.6-0.7	5306
0.7-0.8	1127
0.8-0.85	25
0.85-0.9	4
0.9-0.95	1
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 NPC33894 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	183
0.1-0.2	1527
0.2-0.3	3924
0.3-0.4	2417
0.4-0.5	634
0.5-0.6	296
0.6-0.7	146
0.7-0.8	23
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