NPASS Compound

Structure

NPC70463 OpenBabel06302215212D 65 71 0 0 1 0 0 0 0 0999 V2000 -1.7321 0.0000 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 1 0 0 0 0 0 0 0 0 0 0.0000 2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 O 0 0 0 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 3.4641 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.1962 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1962 -0.0000 0.0000 C 0 0 1 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 6.0622 0.5000 0.0000 O 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 5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 3.0000 0.0000 O 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 7.7942 1.5000 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 9.5263 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 6.0000 0.0000 O 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 6.0622 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.9282 -3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.9282 -4.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.0622 -4.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1962 -4.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3301 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -4.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -4.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -5.5000 0.0000 O 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 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 62 1 0 0 0 0 3 4 1 0 0 0 0 3 65 1 6 0 0 0 4 5 1 0 0 0 0 4 64 1 1 0 0 0 5 6 1 0 0 0 0 5 63 1 1 0 0 0 6 7 1 6 0 0 0 6 62 1 0 0 0 0 7 8 1 0 0 0 0 9 8 1 1 0 0 0 9 10 1 0 0 0 0 9 14 1 0 0 0 0 10 11 1 0 0 0 0 10 61 1 1 0 0 0 11 12 1 0 0 0 0 11 50 1 1 0 0 0 12 13 1 0 0 0 0 12 36 1 6 0 0 0 13 14 1 0 0 0 0 13 15 1 1 0 0 0 15 16 1 0 0 0 0 16 26 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 24 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 35 1 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 34 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 32 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 30 31 2 0 0 0 0 30 33 1 0 0 0 0 31 32 1 0 0 0 0 37 36 1 1 0 0 0 37 38 1 0 0 0 0 37 43 1 0 0 0 0 38 39 1 0 0 0 0 38 49 1 6 0 0 0 39 40 1 0 0 0 0 39 48 1 6 0 0 0 40 41 1 0 0 0 0 40 44 1 1 0 0 0 41 42 1 6 0 0 0 41 43 1 0 0 0 0 44 45 1 0 0 0 0 45 46 2 0 0 0 0 45 47 1 0 0 0 0 51 50 1 1 0 0 0 51 52 1 0 0 0 0 51 58 1 0 0 0 0 52 53 1 0 0 0 0 53 54 1 0 0 0 0 53 60 1 6 0 0 0 54 55 1 0 0 0 0 54 59 1 1 0 0 0 55 56 1 1 0 0 0 55 58 1 0 0 0 0 56 57 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	928.28
Volume:	845.034
LogP:	-0.122
LogD:	-0.186
LogS:	-3.201
# Rotatable Bonds:	13
TPSA:	373.11
# H-Bond Aceptor:	24
# H-Bond Donor:	12
# Rings:	7
# Heavy Atoms:	24

MedChem Properties

QED Drug-Likeness Score:	0.08
Synthetic Accessibility Score:	5.995
Fsp3:	0.61
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.54
MDCK Permeability:	0.00018122865003533661
Pgp-inhibitor:	0.0
Pgp-substrate:	1.0
Human Intestinal Absorption (HIA):	0.958
20% Bioavailability (F20%):	0.001
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.284
Plasma Protein Binding (PPB):	68.48371124267578%
Volume Distribution (VD):	0.45
Pgp-substrate:	25.791566848754883%

ADMET: Metabolism

CYP1A2-inhibitor:	0.007
CYP1A2-substrate:	0.024
CYP2C19-inhibitor:	0.018
CYP2C19-substrate:	0.051
CYP2C9-inhibitor:	0.001
CYP2C9-substrate:	0.034
CYP2D6-inhibitor:	0.029
CYP2D6-substrate:	0.074
CYP3A4-inhibitor:	0.041
CYP3A4-substrate:	0.002

ADMET: Excretion

Clearance (CL):	0.467
Half-life (T1/2):	0.731

ADMET: Toxicity

hERG Blockers:	0.527
Human Hepatotoxicity (H-HT):	0.148
Drug-inuced Liver Injury (DILI):	0.988
AMES Toxicity:	0.729
Rat Oral Acute Toxicity:	0.034
Maximum Recommended Daily Dose:	0.006
Skin Sensitization:	0.788
Carcinogencity:	0.086
Eye Corrosion:	0.003
Eye Irritation:	0.017
Respiratory Toxicity:	0.051

Download Data

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

Natural Product: NPC70463

Natural Product ID:	NPC70463
*Common Name:**	UPRISLONVRWIDG-ZJDHXBILSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	UPRISLONVRWIDG-ZJDHXBILSA-N
Standard InCHI:	InChI=1S/C41H52O24/c1-13-26(48)30(52)32(54)39(57-13)56-12-23-28(50)36(63-24-10-20(47)27(49)22(11-42)60-24)38(65-40-33(55)31(53)34(14(2)58-40)59-15(3)43)41(62-23)64-37-29(51)25-19(46)8-18(45)9-21(25)61-35(37)16-4-6-17(44)7-5-16/h4-9,13-14,20,22-24,26-28,30-34,36,38-42,44-50,52-55H,10-12H2,1-3H3/t13-,14-,20-,22+,23+,24-,26-,27+,28-,30+,31-,32+,33+,34-,36-,38+,39+,40-,41-/m0/s1
SMILES:	C[C@H]1[C@@H]([C@H]([C@H]([C@H](OC[C@@H]2[C@@H]([C@@H]([C@H]([C@@H](O2)Oc2c(=O)c3c(cc(cc3oc2c2ccc(cc2)O)O)O)O[C@H]2[C@@H]([C@@H]([C@H]([C@H](C)O2)OC(=O)C)O)O)O[C@H]2C[C@@H]([C@H]([C@@H](CO)O2)O)O)O)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003531] Flavonoid-3-O-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
NPO17211	Albizia inundata	Species	Fabaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[21314099]
NPO17211	Albizia inundata	Species	Fabaceae	Eukaryota	aerial parts	Primavera, Department Patino, Province of Formosa, Argentina (lat. 27S, long. 58W)	1999-AUG	PMID[21314099]
NPO8416	Picrorhiza kurrooa	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16799	Glinus lotoides	Species	Molluginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8416	Picrorhiza kurrooa	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8416	Picrorhiza kurrooa	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO16799	Glinus lotoides	Species	Molluginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12946	Onobrychis cyri	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17211	Albizia inundata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8416	Picrorhiza kurrooa	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17367	Parmelia subrudecta	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14256	Acnistus breviflorus	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12607	Ircinia dendroides	Species	Irciniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO534	Nassauvia cumingii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17834	Tipuana tipu	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14521	Oxalis purpurea	Species	Oxalidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17293	Menegazzia asahinae	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4960	Garrya elliptica	Species	Garryaceae	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 NPC70463 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	432
0.1-0.2	1743
0.2-0.3	4077
0.3-0.4	9083
0.4-0.5	8958
0.5-0.6	5764
0.6-0.7	5866
0.7-0.8	5432
0.8-0.85	631
0.85-0.9	459
0.9-0.95	215
0.95-1	37

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 NPC70463 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	952
0.2-0.3	2018
0.3-0.4	2771
0.4-0.5	1869
0.5-0.6	808
0.6-0.7	227
0.7-0.8	102
0.8-0.85	17
0.85-0.9	6
0.9-0.95	3
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