NPASS Compound

Structure

NPC97953 OpenBabel06302215402D 35 39 0 0 1 0 0 0 0 0999 V2000 1.4228 -4.1073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9485 -3.2858 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.2858 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4228 -2.4644 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9485 -1.6429 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4228 -0.8215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9485 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 0.9485 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9485 0.9485 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4743 -0.8215 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3905 -0.5760 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.2120 -1.0502 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9433 -1.3216 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1871 -2.0625 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.7598 -2.7151 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5575 -3.2283 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9832 -2.7879 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0670 -3.0334 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.2455 -2.5591 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5070 -3.1366 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.6429 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8763 -1.2799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9432 -3.9738 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4575 -1.9665 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.3159 -1.5855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0752 -2.2871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2620 -2.7498 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5483 -3.6309 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1275 -2.1863 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5143 0.3645 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8324 -0.4910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5032 0.1797 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4194 -0.0658 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2577 1.0959 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 6 1 0 0 0 0 5 22 1 0 0 0 0 7 6 1 6 0 0 0 7 8 1 0 0 0 0 7 10 1 0 0 0 0 8 9 1 0 0 0 0 8 11 1 0 0 0 0 8 32 1 1 0 0 0 9 10 1 0 0 0 0 11 12 1 0 0 0 0 11 22 1 0 0 0 0 12 13 1 0 0 0 0 12 31 1 1 0 0 0 13 14 1 1 0 0 0 13 25 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 30 1 0 0 0 0 16 28 1 0 0 0 0 16 17 1 6 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 18 25 1 0 0 0 0 18 29 1 0 0 0 0 19 20 1 0 0 0 0 19 24 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 22 23 1 6 0 0 0 25 26 1 0 0 0 0 25 27 1 0 0 0 0 27 28 1 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 33 35 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	498.21
Volume:	469.661
LogP:	0.74
LogD:	-0.13
LogS:	-3.422
# Rotatable Bonds:	4
TPSA:	169.05
# H-Bond Aceptor:	11
# H-Bond Donor:	4
# Rings:	5
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.339
Synthetic Accessibility Score:	6.577
Fsp3:	0.875
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-5.571
MDCK Permeability:	0.0001117341234930791
Pgp-inhibitor:	0.016
Pgp-substrate:	0.999
Human Intestinal Absorption (HIA):	0.819
20% Bioavailability (F20%):	0.984
30% Bioavailability (F30%):	0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.087
Plasma Protein Binding (PPB):	27.081787109375%
Volume Distribution (VD):	0.612
Pgp-substrate:	60.68463134765625%

ADMET: Metabolism

CYP1A2-inhibitor:	0.001
CYP1A2-substrate:	0.112
CYP2C19-inhibitor:	0.005
CYP2C19-substrate:	0.688
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.005
CYP2D6-inhibitor:	0.005
CYP2D6-substrate:	0.058
CYP3A4-inhibitor:	0.041
CYP3A4-substrate:	0.212

ADMET: Excretion

Clearance (CL):	1.875
Half-life (T1/2):	0.754

ADMET: Toxicity

hERG Blockers:	0.48
Human Hepatotoxicity (H-HT):	0.965
Drug-inuced Liver Injury (DILI):	0.773
AMES Toxicity:	0.149
Rat Oral Acute Toxicity:	0.951
Maximum Recommended Daily Dose:	0.986
Skin Sensitization:	0.405
Carcinogencity:	0.057
Eye Corrosion:	0.003
Eye Irritation:	0.013
Respiratory Toxicity:	0.972

Download Data

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

Natural Product: NPC97953

Natural Product ID:	NPC97953
*Common Name:**	RFSLPOAJKCLJFP-LXKJXWLBSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RFSLPOAJKCLJFP-LXKJXWLBSA-N
Standard InCHI:	InChI=1S/C24H34O11/c1-10(25)34-14-7-15-23(9-32-15,35-11(2)26)17-16(28)12-6-13(27)22(5)24(31,20(12,3)8-33-22)19(30)18(29)21(14,17)4/h12-17,19,27-28,30-31H,6-9H2,1-5H3/t12-,13-,14-,15+,16+,17-,19-,20-,21+,22+,23-,24-/m0/s1
SMILES:	CC(=O)O[C@H]1C[C@@H]2[C@@](CO2)([C@H]2[C@@H]([C@@H]3C[C@@H]([C@]4(C)[C@]([C@H](C(=O)[C@]12C)O)([C@@]3(C)CO4)O)O)O)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001729] Oxepanes

*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
NPO11132	Alangium longiflorum	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30106296]
NPO10084	Equisetum hyemale	Species	Equisetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15125.1	Taxus wallichiana var. chinensis	Varieties	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27451	Ophiocordyceps sinensis	Species	Ophiocordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10084	Equisetum hyemale	Species	Equisetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO27451	Ophiocordyceps sinensis	Species	Ophiocordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO563	Leucopaxillus cerealis	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11132	Alangium longiflorum	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10487	Rosa americana	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10953	Papaver strigosum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27451	Ophiocordyceps sinensis	Species	Ophiocordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22296	Rheum tataricum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15125.1	Taxus wallichiana var. chinensis	Varieties	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10084	Equisetum hyemale	Species	Equisetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11819	Trichophyton megnini	Species	Arthrodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7785	Boletus fomentarius	Species	Boletaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12272	Calceolaria petiolaris	Species	Calceolariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21703	Maianthemum atropurpureum	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12615	Athrotaxis selaginoides	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11936	Ptilocaulis walpersi	Species	Axinellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3362	Dictyostelium mucoroides	Species	n.a.	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 NPC97953 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	501
0.1-0.2	3531
0.2-0.3	8051
0.3-0.4	13689
0.4-0.5	7458
0.5-0.6	6483
0.6-0.7	2577
0.7-0.8	391
0.8-0.85	7
0.85-0.9	9
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 NPC97953 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	544
0.1-0.2	3697
0.2-0.3	3195
0.3-0.4	1005
0.4-0.5	389
0.5-0.6	232
0.6-0.7	86
0.7-0.8	2
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