NPASS Compound

Structure

NPC274422 OpenBabel06302215232D 36 38 0 0 1 0 0 0 0 0999 V2000 5.1962 5.0000 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 3.4641 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.4641 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 2 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 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 1.7321 -1.0000 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 0 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 0.0000 C 0 0 0 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 -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 -2.5981 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3336 2.9914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1712 2.7071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1371 2.4483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3960 1.4824 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.6888 0.7753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4300 -0.1907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3960 0.0681 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7229 1.0341 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.3619 1.2235 0.0000 Br 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 -0.0000 0.0000 O 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 3.9641 3.8660 0.0000 O 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 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 36 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 6 0 0 0 6 8 1 0 0 0 0 6 35 1 0 0 0 0 8 9 1 0 0 0 0 8 34 1 1 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 13 11 1 6 0 0 0 13 14 1 0 0 0 0 13 33 1 0 0 0 0 14 15 1 0 0 0 0 16 15 1 6 0 0 0 16 17 1 0 0 0 0 16 32 1 0 0 0 0 17 18 1 6 0 0 0 17 19 1 0 0 0 0 17 33 1 0 0 0 0 19 20 1 0 0 0 0 21 20 1 6 0 0 0 21 22 1 0 0 0 0 21 32 1 0 0 0 0 22 30 1 0 0 0 0 22 23 1 6 0 0 0 22 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 26 31 1 6 0 0 0 27 28 1 0 0 0 0 27 29 1 0 0 0 0 27 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	570.29
Volume:	559.728
LogP:	6.707
LogD:	4.494
LogS:	-5.554
# Rotatable Bonds:	9
TPSA:	68.15
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.236
Synthetic Accessibility Score:	5.329
Fsp3:	0.867
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected
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:	-4.701
MDCK Permeability:	1.520741807325976e-05
Pgp-inhibitor:	0.983
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.149
30% Bioavailability (F30%):	0.316

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.079
Plasma Protein Binding (PPB):	98.58409881591797%
Volume Distribution (VD):	1.411
Pgp-substrate:	6.743214130401611%

ADMET: Metabolism

CYP1A2-inhibitor:	0.016
CYP1A2-substrate:	0.367
CYP2C19-inhibitor:	0.085
CYP2C19-substrate:	0.895
CYP2C9-inhibitor:	0.38
CYP2C9-substrate:	0.043
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.141
CYP3A4-inhibitor:	0.408
CYP3A4-substrate:	0.623

ADMET: Excretion

Clearance (CL):	7.867
Half-life (T1/2):	0.049

ADMET: Toxicity

hERG Blockers:	0.653
Human Hepatotoxicity (H-HT):	0.969
Drug-inuced Liver Injury (DILI):	0.248
AMES Toxicity:	0.048
Rat Oral Acute Toxicity:	0.712
Maximum Recommended Daily Dose:	0.662
Skin Sensitization:	0.355
Carcinogencity:	0.423
Eye Corrosion:	0.004
Eye Irritation:	0.027
Respiratory Toxicity:	0.911

Download Data

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

Natural Product: NPC274422

Natural Product ID:	NPC274422
*Common Name:**	DGGUAYSXQZKRPV-CIXNMJELSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DGGUAYSXQZKRPV-CIXNMJELSA-N
Standard InCHI:	InChI=1S/C30H51BrO5/c1-20(2)10-9-17-28(6,33)24(32)13-11-21(3)22-12-14-25-29(7,35-22)19-16-26(34-25)30(8)18-15-23(31)27(4,5)36-30/h10,22-26,32-33H,3,9,11-19H2,1-2,4-8H3/t22-,23-,24+,25-,26-,28-,29+,30+/m1/s1
SMILES:	CC(=CCC[C@](C)([C@H](CCC(=C)[C@H]1CC[C@@H]2[C@](C)(CC[C@H]([C@]3(C)CC[C@H](C(C)(C)O3)Br)O2)O1)O)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	23425823
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
NPO8821	Delphinium dictyocarpum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8821	Delphinium dictyocarpum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2491	Laurencia obtusa	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO666	Cymbidium aloifolium	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5527	Ligularia atroviolacea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10341	Pseudogymnoascus pannorum	Species	Pseudeurotiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2491	Laurencia obtusa	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8821	Delphinium dictyocarpum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1054	Peucedanum graveolens	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18938	Ladeania juncea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15600	Trifolium pannonicum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13493	Mauremys reevesii	Species	Geoemydidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2329	Scutellaria glabra	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1221	Juniperus serawschanica	Species	Cupressaceae	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 NPC274422 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	197
0.1-0.2	1600
0.2-0.3	5492
0.3-0.4	15047
0.4-0.5	10887
0.5-0.6	7836
0.6-0.7	1590
0.7-0.8	45
0.8-0.85	2
0.85-0.9	0
0.9-0.95	1
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 NPC274422 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	178
0.1-0.2	1849
0.2-0.3	4146
0.3-0.4	2195
0.4-0.5	528
0.5-0.6	223
0.6-0.7	31
0.7-0.8	0
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