NPASS Compound

Structure

NPC144191 OpenBabel06302216202D 32 32 0 0 0 0 0 0 0 0999 V2000 11.2583 14.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 15.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 14.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 13.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 13.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 11.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 8.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 7.5000 0.0000 C 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 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 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 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 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 2.5981 1.5000 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 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 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 -0.0000 -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 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 -0.8660 -0.5000 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 -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 0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 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 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 29 2 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 25 26 1 0 0 0 0 25 32 1 0 0 0 0 26 27 1 0 0 0 0 26 28 2 0 0 0 0 28 29 1 0 0 0 0 28 30 1 0 0 0 0 30 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	518.4
Volume:	566.48
LogP:	6.991
LogD:	5.708
LogS:	-5.943
# Rotatable Bonds:	9
TPSA:	72.83
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.37
Synthetic Accessibility Score:	4.832
Fsp3:	0.938
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.69
MDCK Permeability:	1.9921153580071405e-05
Pgp-inhibitor:	0.998
Pgp-substrate:	0.014
Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.933
30% Bioavailability (F30%):	0.747

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.043
Plasma Protein Binding (PPB):	94.28038787841797%
Volume Distribution (VD):	1.176
Pgp-substrate:	1.4721968173980713%

ADMET: Metabolism

CYP1A2-inhibitor:	0.039
CYP1A2-substrate:	0.078
CYP2C19-inhibitor:	0.044
CYP2C19-substrate:	0.779
CYP2C9-inhibitor:	0.191
CYP2C9-substrate:	0.162
CYP2D6-inhibitor:	0.009
CYP2D6-substrate:	0.128
CYP3A4-inhibitor:	0.48
CYP3A4-substrate:	0.494

ADMET: Excretion

Clearance (CL):	3.797
Half-life (T1/2):	0.076

ADMET: Toxicity

hERG Blockers:	0.874
Human Hepatotoxicity (H-HT):	0.252
Drug-inuced Liver Injury (DILI):	0.946
AMES Toxicity:	0.015
Rat Oral Acute Toxicity:	0.003
Maximum Recommended Daily Dose:	0.044
Skin Sensitization:	0.98
Carcinogencity:	0.1
Eye Corrosion:	0.935
Eye Irritation:	0.297
Respiratory Toxicity:	0.7

Download Data

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

Natural Product: NPC144191

Natural Product ID:	NPC144191
*Common Name:**	ZDTSGGWIINUOER-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZDTSGGWIINUOER-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C30H54O2/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-23-24-28-25-29(31)27(2)30(26-28)32-3/h25-26,31H,4-24H2,1-3H3
SMILES:	CCCCCCCCCCCCCCCCCCCCCCc1cc(c(C)c(c1)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	86213877
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000134] Phenols [CHEMONTID:0000190] Methoxyphenols

*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
NPO7294	Cunninghamella echinulata	Species	Cunninghamellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12740180]
NPO10946	Pseudallescheria boydii	Species	Microascaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20509707]
NPO19556	Clathrina clathrus	Species	Clathrinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[20590100]
NPO10946	Pseudallescheria boydii	Species	Microascaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23964677]
NPO20453	Cayratia japonica	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20453	Cayratia japonica	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15736	Liatris spicata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15736	Liatris spicata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10946	Pseudallescheria boydii	Species	Microascaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22090	Aframomum alboviolaceum	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7294	Cunninghamella echinulata	Species	Cunninghamellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15736	Liatris spicata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19556	Clathrina clathrus	Species	Clathrinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20453	Cayratia japonica	Species	Vitaceae	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 NPC144191 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	312
0.1-0.2	1632
0.2-0.3	4818
0.3-0.4	13791
0.4-0.5	4565
0.5-0.6	5748
0.6-0.7	8367
0.7-0.8	2902
0.8-0.85	419
0.85-0.9	114
0.9-0.95	29
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 NPC144191 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	309
0.1-0.2	1031
0.2-0.3	1742
0.3-0.4	2787
0.4-0.5	1634
0.5-0.6	1041
0.6-0.7	521
0.7-0.8	73
0.8-0.85	7
0.85-0.9	5
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