NPASS Compound

Structure

NPC172434 OpenBabel06302216202D 31 35 0 0 1 0 0 0 0 0999 V2000 -0.1242 -4.6336 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0791 -5.5886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6463 -6.2421 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0078 -5.8900 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.2110 -6.8450 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7332 -5.2365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6619 -5.5379 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3873 -4.8844 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3160 -5.1859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3870 -3.9080 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2322 -3.4191 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2319 -2.4423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5401 -2.4428 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6935 -1.9543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8472 -2.4433 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8474 -3.4200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6941 -3.9085 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5404 -3.4196 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5407 -4.4196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0005 -1.9548 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0008 -2.9548 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8452 -2.4437 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6912 -1.9553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6915 -0.9779 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8458 -0.4890 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0003 -0.9774 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8466 -0.4885 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6932 -0.9769 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5591 -0.4767 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 -2.5577 -0.4783 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 2 4 1 0 0 0 0 4 5 1 6 0 0 0 4 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 1 6 0 0 0 10 8 1 6 0 0 0 10 11 1 0 0 0 0 10 18 1 0 0 0 0 11 12 1 0 0 0 0 13 12 1 6 0 0 0 13 14 1 0 0 0 0 13 18 1 0 0 0 0 14 28 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 15 20 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 6 0 0 0 20 26 1 0 0 0 0 20 21 1 6 0 0 0 20 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 24 31 1 6 0 0 0 26 25 1 6 0 0 0 26 30 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 27 30 1 1 0 0 0 28 29 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	428.33
Volume:	471.16
LogP:	5.07
LogD:	4.624
LogS:	-5.152
# Rotatable Bonds:	4
TPSA:	52.99
# H-Bond Aceptor:	3
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.449
Synthetic Accessibility Score:	5.682
Fsp3:	0.857
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.865
MDCK Permeability:	3.2882649975363165e-05
Pgp-inhibitor:	0.022
Pgp-substrate:	0.957
Human Intestinal Absorption (HIA):	0.013
20% Bioavailability (F20%):	0.767
30% Bioavailability (F30%):	0.57

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.047
Plasma Protein Binding (PPB):	86.32112884521484%
Volume Distribution (VD):	1.148
Pgp-substrate:	1.8548341989517212%

ADMET: Metabolism

CYP1A2-inhibitor:	0.032
CYP1A2-substrate:	0.751
CYP2C19-inhibitor:	0.056
CYP2C19-substrate:	0.941
CYP2C9-inhibitor:	0.256
CYP2C9-substrate:	0.063
CYP2D6-inhibitor:	0.011
CYP2D6-substrate:	0.175
CYP3A4-inhibitor:	0.812
CYP3A4-substrate:	0.871

ADMET: Excretion

Clearance (CL):	3.074
Half-life (T1/2):	0.134

ADMET: Toxicity

hERG Blockers:	0.014
Human Hepatotoxicity (H-HT):	0.152
Drug-inuced Liver Injury (DILI):	0.037
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.777
Maximum Recommended Daily Dose:	0.945
Skin Sensitization:	0.039
Carcinogencity:	0.005
Eye Corrosion:	0.004
Eye Irritation:	0.041
Respiratory Toxicity:	0.957

Download Data

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

Natural Product: NPC172434

Natural Product ID:	NPC172434
*Common Name:**	PCIZFQVDNDHRPP-WOIVZMLFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PCIZFQVDNDHRPP-WOIVZMLFSA-N
Standard InCHI:	InChI=1S/C28H44O3/c1-16(2)17(3)7-8-18(4)20-9-10-21-23-22(12-13-26(20,21)5)27(6)14-11-19(29)15-28(27)25(31-28)24(23)30/h7-8,16-21,24-25,29-30H,9-15H2,1-6H3/b8-7+/t17-,18+,19-,20+,21-,24-,25-,26+,27+,28-/m0/s1
SMILES:	CC(C)[C@@H](C)/C=C/[C@@H](C)[C@H]1CC[C@H]2C3=C(CC[C@]12C)[C@@]1(C)CC[C@@H](C[C@@]21[C@H]([C@H]3O)O2)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	12019948
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0003567] Ergostane steroids

*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
NPO3499	Macaranga conifera	Species	Euphorbiaceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1016/S0031-9422(02)00378-3]
NPO14094	Aspergillus ochraceus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11170686]
NPO14094	Aspergillus ochraceus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16156520]
NPO14094	Aspergillus ochraceus	Species	Aspergillaceae	Eukaryota	n.a.	mycelium	n.a.	PMID[21043476]
NPO19186	Penicillium commune	Species	Aspergillaceae	Eukaryota	n.a.	mycelium	n.a.	PMID[21226488]
NPO3499	Macaranga conifera	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21275386]
NPO3499	Macaranga conifera	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3499	Macaranga conifera	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3499	Macaranga conifera	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2271	Cassia reticulata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28869	Neonectria obtusispora	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19186	Penicillium commune	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO370	Rhizophora apiculata	Species	Rhizophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8684	Nymphaea ampla	Species	Nymphaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6631	Elaeagnus glabra	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19426	Diospyros ferrea	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO155	Artemisia lanata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5288	Stomatanthes corumbensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14094	Aspergillus ochraceus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4483	Ganonema farinosum	Species	Liagoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9378	Halocynthia aurantium	Species	Pyuridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1779	Sargassum kjellmanianum	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11051	Nicotiana cavicola	Species	Solanaceae	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 NPC172434 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	200
0.1-0.2	1439
0.2-0.3	4987
0.3-0.4	12208
0.4-0.5	11164
0.5-0.6	7297
0.6-0.7	4544
0.7-0.8	808
0.8-0.85	36
0.85-0.9	10
0.9-0.95	2
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 NPC172434 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	184
0.1-0.2	1736
0.2-0.3	4121
0.3-0.4	2154
0.4-0.5	558
0.5-0.6	244
0.6-0.7	133
0.7-0.8	20
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