NPASS Compound

Structure

NPC254517 OpenBabel06302215402D 44 47 0 0 1 0 0 0 0 0999 V2000 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 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 0 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 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 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 1.0000 0.0000 C 0 0 1 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 -6.9282 1.0000 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 -7.7942 2.5000 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 -6.0622 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 4.0000 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 -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 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 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 -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 1 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 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 0.0000 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -4.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3660 -5.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -6.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -6.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8660 -4.5000 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 2.5981 -0.5000 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 0.8660 2.5000 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 1 2 1 0 0 0 0 2 21 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 3 44 1 0 0 0 0 4 18 1 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 1 0 0 0 8 17 1 0 0 0 0 9 14 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 15 1 0 0 0 0 13 14 1 0 0 0 0 15 16 1 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 23 22 1 1 0 0 0 23 24 1 0 0 0 0 23 40 1 0 0 0 0 24 25 1 0 0 0 0 24 43 1 6 0 0 0 25 26 1 0 0 0 0 25 42 1 1 0 0 0 26 27 1 0 0 0 0 26 41 1 6 0 0 0 27 28 1 1 0 0 0 27 40 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 30 32 1 0 0 0 0 32 33 1 0 0 0 0 33 34 1 6 0 0 0 33 35 1 0 0 0 0 33 39 1 0 0 0 0 35 36 1 0 0 0 0 36 37 2 0 0 0 0 36 38 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	620.21
Volume:	592.545
LogP:	1.976
LogD:	0.569
LogS:	-3.442
# Rotatable Bonds:	11
TPSA:	218.74
# H-Bond Aceptor:	14
# H-Bond Donor:	6
# Rings:	4
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.205
Synthetic Accessibility Score:	4.607
Fsp3:	0.5
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:	-6.098
MDCK Permeability:	2.3719831006019376e-05
Pgp-inhibitor:	0.009
Pgp-substrate:	0.996
Human Intestinal Absorption (HIA):	0.073
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.983

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.075
Plasma Protein Binding (PPB):	83.07862854003906%
Volume Distribution (VD):	0.373
Pgp-substrate:	9.360718727111816%

ADMET: Metabolism

CYP1A2-inhibitor:	0.012
CYP1A2-substrate:	0.106
CYP2C19-inhibitor:	0.025
CYP2C19-substrate:	0.264
CYP2C9-inhibitor:	0.021
CYP2C9-substrate:	0.771
CYP2D6-inhibitor:	0.017
CYP2D6-substrate:	0.147
CYP3A4-inhibitor:	0.057
CYP3A4-substrate:	0.103

ADMET: Excretion

Clearance (CL):	6.217
Half-life (T1/2):	0.688

ADMET: Toxicity

hERG Blockers:	0.152
Human Hepatotoxicity (H-HT):	0.595
Drug-inuced Liver Injury (DILI):	0.934
AMES Toxicity:	0.191
Rat Oral Acute Toxicity:	0.205
Maximum Recommended Daily Dose:	0.334
Skin Sensitization:	0.225
Carcinogencity:	0.243
Eye Corrosion:	0.003
Eye Irritation:	0.011
Respiratory Toxicity:	0.044

Download Data

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

Natural Product: NPC254517

Natural Product ID:	NPC254517
*Common Name:**	SMLRKPPCBXFZQW-JNMJVINGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SMLRKPPCBXFZQW-JNMJVINGSA-N
Standard InCHI:	InChI=1S/C30H36O14/c1-13-23(35)22-17(31)9-18(15-5-7-16(40-4)8-6-15)42-28(22)14(2)27(13)44-29-26(38)25(37)24(36)19(43-29)12-41-21(34)11-30(3,39)10-20(32)33/h5-8,18-19,24-26,29,35-39H,9-12H2,1-4H3,(H,32,33)/t18-,19+,24+,25-,26+,29-,30-/m0/s1
SMILES:	Cc1c(c2C(=O)C[C@@H](c3ccc(cc3)OC)Oc2c(C)c1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](COC(=O)C[C@](C)(CC(=O)O)O)O1)O)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:0003533] Flavonoid-7-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
NPO5638	Garcinia livingstonei	Species	Clusiaceae	Eukaryota	n.a.	fruit	n.a.	DOI[10.1016/S0040-4020(01)89039-6]
NPO4703	Solanum hispidum	Species	Solanaceae	Eukaryota	leaves	n.a.	n.a.	PMID[15217270]
NPO46	Onosma hispida	Species	Boraginaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[16079517]
NPO5638	Garcinia livingstonei	Species	Clusiaceae	Eukaryota	root bark	n.a.	n.a.	PMID[16562837]
NPO5638	Garcinia livingstonei	Species	Clusiaceae	Eukaryota	n.a.	fruit	n.a.	PMID[21028890]
NPO14359	Pentarhizidium orientale	Species	Onocleaceae	Eukaryota	Rhizomes	n.a.	n.a.	PMID[28984452]
NPO46	Onosma hispida	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO46	Onosma hispida	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14359	Pentarhizidium orientale	Species	Onocleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3789	Lyonia formosa	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14359	Pentarhizidium orientale	Species	Onocleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5638	Garcinia livingstonei	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27945	Cancrinia discoidea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1896	Proteus penneri	Species	Morganellaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO46	Onosma hispida	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4703	Solanum hispidum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2828	Blaps mucronata	Species	Tenebrionidae	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 NPC254517 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	368
0.1-0.2	1490
0.2-0.3	3377
0.3-0.4	7917
0.4-0.5	10241
0.5-0.6	4835
0.6-0.7	5476
0.7-0.8	5895
0.8-0.85	2250
0.85-0.9	749
0.9-0.95	97
0.95-1	2

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 NPC254517 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	315
0.1-0.2	877
0.2-0.3	1750
0.3-0.4	2620
0.4-0.5	1993
0.5-0.6	1068
0.6-0.7	339
0.7-0.8	147
0.8-0.85	32
0.85-0.9	9
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