NPASS Compound

Structure

NPC193830 OpenBabel06302215132D 22 22 0 0 1 0 0 0 0 0999 V2000 -3.4641 -3.0000 0.0000 C 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 -2.5981 -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 -1.7321 -3.0000 0.0000 O 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 -0.8660 -0.5000 0.0000 C 0 0 2 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 -1.7321 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 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 -0.3660 2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3660 2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0000 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 0.8660 -0.5000 0.0000 C 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 -5.1962 -2.0000 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 -6.0622 -0.5000 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 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 18 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 6 1 0 0 0 0 7 6 1 6 0 0 0 7 8 1 0 0 0 0 7 16 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 9 12 1 0 0 0 0 10 11 2 0 0 0 0 12 13 1 0 0 0 0 12 14 1 0 0 0 0 12 15 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	685.51
Volume:	739.447
LogP:	6.555
LogD:	4.665
LogS:	-2.733
# Rotatable Bonds:	31
TPSA:	168.94
# H-Bond Aceptor:	10
# H-Bond Donor:	7
# Rings:	1
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.039
Synthetic Accessibility Score:	4.661
Fsp3:	0.868
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:	-5.476
MDCK Permeability:	8.214305125875399e-06
Pgp-inhibitor:	0.123
Pgp-substrate:	0.221
Human Intestinal Absorption (HIA):	0.953
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.013
Plasma Protein Binding (PPB):	99.63558197021484%
Volume Distribution (VD):	0.739
Pgp-substrate:	1.9594881534576416%

ADMET: Metabolism

CYP1A2-inhibitor:	0.015
CYP1A2-substrate:	0.092
CYP2C19-inhibitor:	0.139
CYP2C19-substrate:	0.043
CYP2C9-inhibitor:	0.137
CYP2C9-substrate:	0.99
CYP2D6-inhibitor:	0.009
CYP2D6-substrate:	0.043
CYP3A4-inhibitor:	0.168
CYP3A4-substrate:	0.008

ADMET: Excretion

Clearance (CL):	1.796
Half-life (T1/2):	0.633

ADMET: Toxicity

hERG Blockers:	0.275
Human Hepatotoxicity (H-HT):	0.146
Drug-inuced Liver Injury (DILI):	0.008
AMES Toxicity:	0.018
Rat Oral Acute Toxicity:	0.028
Maximum Recommended Daily Dose:	0.035
Skin Sensitization:	0.96
Carcinogencity:	0.009
Eye Corrosion:	0.003
Eye Irritation:	0.013
Respiratory Toxicity:	0.473

Download Data

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

Natural Product: NPC193830

Natural Product ID:	NPC193830
*Common Name:**	RYGKALGARMELFA-KDHUCADRSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RYGKALGARMELFA-KDHUCADRSA-N
Standard InCHI:	InChI=1S/C17H22O5/c1-11(10-21-13(3)19)6-16(20)22-15-7-14(9-18)17(4,5)8-12(15)2/h6-9,15H,10H2,1-5H3/b11-6+/t15-/m1/s1
SMILES:	C/C(=CC(=O)O[C@@H]1C=C(C=O)C(C)(C)C=C1C)/COC(=O)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:0003909] Fatty Acyls [CHEMONTID:0000324] Fatty acid esters

*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
NPO18781	Hyoscyamus niger	Species	Solanaceae	Eukaryota	seeds	n.a.	n.a.	PMID[11858758]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12350148]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12762798]
NPO15561	Dermacoccus abyssi	Species	Dermacoccaceae	Bacteria	n.a.	n.a.	n.a.	PMID[20448892]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21044847]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	n.a.	root	n.a.	PMID[21973054]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	roots	n.a.	n.a.	PMID[21973054]
NPO15561	Dermacoccus abyssi	Species	Dermacoccaceae	Bacteria	n.a.	Mariana Trench sediments	n.a.	PMID[24499261]
NPO19028	Dysidea granulosa	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[25863431]
NPO19028	Dysidea granulosa	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[27399938]
NPO19028	Dysidea granulosa	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[31990554]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12908	Euchresta japonica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18781	Hyoscyamus niger	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12908	Euchresta japonica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18781	Hyoscyamus niger	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18781	Hyoscyamus niger	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18781	Hyoscyamus niger	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12908	Euchresta japonica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18781	Hyoscyamus niger	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15561	Dermacoccus abyssi	Species	Dermacoccaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO6172	Scorzonera laciniata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19028	Dysidea granulosa	Species	n.a.	n.a.	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 NPC193830 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	171
0.1-0.2	3901
0.2-0.3	16195
0.3-0.4	12538
0.4-0.5	6595
0.5-0.6	2884
0.6-0.7	374
0.7-0.8	38
0.8-0.85	1
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 NPC193830 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	157
0.1-0.2	3805
0.2-0.3	3913
0.3-0.4	953
0.4-0.5	254
0.5-0.6	61
0.6-0.7	6
0.7-0.8	1
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