NPASS Compound

Structure

NPC301015 OpenBabel06302215532D 64 70 0 0 1 0 0 0 0 0999 V2000 11.2583 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 1.0000 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 3.4641 0.0000 0.0000 C 0 0 1 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 2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 O 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 3.4641 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 O 0 0 0 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 -0.0000 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 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 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 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 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.1614 -0.6738 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3799 -2.1235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3548 -1.9010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9182 -2.7272 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9154 -2.6525 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3492 -1.7515 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.3464 -1.6768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4212 -2.6740 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.2474 -2.1107 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7803 -0.7758 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.2170 0.0504 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2198 -0.0243 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7859 -0.9253 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.2226 -0.0990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7887 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3548 -0.0990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3799 0.1235 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 -8.7775 -0.7011 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.3409 -1.5273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.9070 -2.4283 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.3381 -1.4526 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 1.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -0.8660 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 2 4 1 0 0 0 0 4 5 1 0 0 0 0 5 10 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 8 11 1 0 0 0 0 9 10 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 13 15 1 0 0 0 0 16 15 1 6 0 0 0 16 17 1 0 0 0 0 16 21 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 19 30 1 6 0 0 0 20 21 1 0 0 0 0 20 26 1 1 0 0 0 21 22 1 6 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 23 25 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 31 30 1 6 0 0 0 31 32 1 0 0 0 0 31 62 1 0 0 0 0 32 33 1 0 0 0 0 33 34 1 0 0 0 0 34 57 1 0 0 0 0 34 35 1 6 0 0 0 34 36 1 0 0 0 0 36 37 1 6 0 0 0 36 62 1 0 0 0 0 37 38 1 0 0 0 0 38 39 1 0 0 0 0 39 57 1 0 0 0 0 39 40 1 6 0 0 0 39 41 1 0 0 0 0 41 42 1 0 0 0 0 42 54 1 0 0 0 0 42 43 2 0 0 0 0 43 44 1 0 0 0 0 45 44 1 1 0 0 0 45 46 1 0 0 0 0 45 52 1 0 0 0 0 46 47 1 0 0 0 0 46 48 1 0 0 0 0 46 49 1 0 0 0 0 49 50 1 0 0 0 0 49 58 1 1 0 0 0 50 51 1 0 0 0 0 51 52 1 0 0 0 0 52 53 1 1 0 0 0 52 54 1 0 0 0 0 54 55 1 1 0 0 0 55 56 1 0 0 0 0 57 56 1 6 0 0 0 58 59 1 0 0 0 0 59 60 2 0 0 0 0 59 61 1 0 0 0 0 62 63 1 0 0 0 0 62 64 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	888.5
Volume:	927.171
LogP:	8.086
LogD:	5.223
LogS:	-6.167
# Rotatable Bonds:	14
TPSA:	149.96
# H-Bond Aceptor:	12
# H-Bond Donor:	0
# Rings:	7
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.058
Synthetic Accessibility Score:	5.747
Fsp3:	0.712
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:	-4.964
MDCK Permeability:	4.5774995669489726e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.162
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.376

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.019
Plasma Protein Binding (PPB):	87.3899917602539%
Volume Distribution (VD):	1.676
Pgp-substrate:	3.9120495319366455%

ADMET: Metabolism

CYP1A2-inhibitor:	0.004
CYP1A2-substrate:	0.029
CYP2C19-inhibitor:	0.058
CYP2C19-substrate:	0.067
CYP2C9-inhibitor:	0.094
CYP2C9-substrate:	0.063
CYP2D6-inhibitor:	0.621
CYP2D6-substrate:	0.133
CYP3A4-inhibitor:	0.345
CYP3A4-substrate:	0.501

ADMET: Excretion

Clearance (CL):	1.635
Half-life (T1/2):	0.01

ADMET: Toxicity

hERG Blockers:	0.115
Human Hepatotoxicity (H-HT):	0.754
Drug-inuced Liver Injury (DILI):	0.719
AMES Toxicity:	0.005
Rat Oral Acute Toxicity:	0.02
Maximum Recommended Daily Dose:	0.965
Skin Sensitization:	0.937
Carcinogencity:	0.016
Eye Corrosion:	0.004
Eye Irritation:	0.024
Respiratory Toxicity:	0.899

Download Data

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

Natural Product: NPC301015

Natural Product ID:	NPC301015
*Common Name:**	YDQIPILJJKOWCG-XZUFBIRPSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YDQIPILJJKOWCG-XZUFBIRPSA-N
Standard InCHI:	InChI=1S/C52H72O12/c1-30(53)59-36-16-12-34(13-17-36)14-21-44(57)63-38-29-58-47(46(62-33(4)56)45(38)61-32(3)55)64-43-24-27-52(11)40(49(43,7)8)22-25-50(9)28-35-15-19-39-48(5,6)42(60-31(2)54)23-26-51(39,10)37(35)18-20-41(50)52/h12-17,21,37-43,45-47H,18-20,22-29H2,1-11H3/b21-14+/t37-,38-,39-,40-,41-,42-,43-,45-,46+,47-,50-,51+,52-/m0/s1
SMILES:	CC(=O)Oc1ccc(cc1)/C=C/C(=O)O[C@H]1CO[C@H]([C@@H]([C@H]1OC(=O)C)OC(=O)C)O[C@H]1CC[C@@]2(C)[C@@H](CC[C@@]3(C)CC4=CC[C@H]5C(C)(C)[C@H](CC[C@]5(C)[C@H]4CC[C@H]23)OC(=O)C)C1(C)C
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:0001553] Triterpenoids

*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
NPO12315	Lycopodiella inundata	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3841	Cissus quadrangula	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12278	Borreliella burgdorferi	Species	Borreliaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO12315	Lycopodiella inundata	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO92	Barringtonia butonica	Species	Lecythidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4749	Matricaria caucasica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1023	Laportea crenulata	Species	Urticaceae	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 NPC301015 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	486
0.1-0.2	1628
0.2-0.3	3577
0.3-0.4	8023
0.4-0.5	9192
0.5-0.6	10996
0.6-0.7	7753
0.7-0.8	1016
0.8-0.85	26
0.85-0.9	0
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 NPC301015 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	377
0.1-0.2	931
0.2-0.3	1896
0.3-0.4	2824
0.4-0.5	1885
0.5-0.6	961
0.6-0.7	263
0.7-0.8	13
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