NPASS Compound

Structure

NPC278032 OpenBabel06302216182D 35 39 0 0 1 0 0 0 0 0999 V2000 1.6887 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8444 -0.4875 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8444 -1.4625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.9500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8444 -1.4625 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6887 -1.9500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5331 -1.4625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5331 -0.4875 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2219 -1.4625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6887 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6887 0.9750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5331 1.4625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3775 0.9750 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2219 1.4625 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3775 1.9500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2219 2.4375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0662 2.9250 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.9106 2.4375 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.9106 1.4625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8856 1.4625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3981 0.6181 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0662 0.9750 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.0662 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2219 -0.4875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3775 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3775 -0.9750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9106 -0.4875 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.7550 2.9250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0662 3.9000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8444 -0.4875 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 0.9750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8444 -2.4375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6887 -2.9250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.9250 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 2 1 1 6 0 0 0 2 3 1 0 0 0 0 2 31 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 30 1 0 0 0 0 5 6 1 0 0 0 0 5 33 1 1 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 25 1 0 0 0 0 8 9 1 6 0 0 0 8 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 13 12 1 1 0 0 0 13 14 1 0 0 0 0 13 25 1 0 0 0 0 14 22 1 0 0 0 0 14 15 1 1 0 0 0 14 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 17 29 1 6 0 0 0 18 19 1 0 0 0 0 18 28 1 1 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 22 19 1 1 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 23 27 1 1 0 0 0 24 25 1 0 0 0 0 25 26 1 1 0 0 0 30 10 1 6 0 0 0 30 31 1 0 0 0 0 31 32 1 1 0 0 0 33 34 2 0 0 0 0 33 35 1 0 0 0 0 M CHG 1 35 -1 M END $$$$

Physi-Chem Properties

Molecular Weight:	488.35
Volume:	523.332
LogP:	4.636
LogD:	4.133
LogS:	-4.065
# Rotatable Bonds:	1
TPSA:	97.99
# H-Bond Aceptor:	5
# H-Bond Donor:	4
# Rings:	5
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.388
Synthetic Accessibility Score:	5.146
Fsp3:	0.9
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:	-5.529
MDCK Permeability:	7.181363343988778e-06
Pgp-inhibitor:	0.007
Pgp-substrate:	0.011
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.007
30% Bioavailability (F30%):	0.294

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.045
Plasma Protein Binding (PPB):	93.52137756347656%
Volume Distribution (VD):	0.574
Pgp-substrate:	4.344028949737549%

ADMET: Metabolism

CYP1A2-inhibitor:	0.011
CYP1A2-substrate:	0.373
CYP2C19-inhibitor:	0.007
CYP2C19-substrate:	0.846
CYP2C9-inhibitor:	0.066
CYP2C9-substrate:	0.642
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.088
CYP3A4-inhibitor:	0.328
CYP3A4-substrate:	0.225

ADMET: Excretion

Clearance (CL):	1.892
Half-life (T1/2):	0.205

ADMET: Toxicity

hERG Blockers:	0.012
Human Hepatotoxicity (H-HT):	0.285
Drug-inuced Liver Injury (DILI):	0.041
AMES Toxicity:	0.009
Rat Oral Acute Toxicity:	0.798
Maximum Recommended Daily Dose:	0.192
Skin Sensitization:	0.071
Carcinogencity:	0.023
Eye Corrosion:	0.264
Eye Irritation:	0.131
Respiratory Toxicity:	0.981

Download Data

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

Natural Product: NPC278032

Natural Product ID:	NPC278032
*Common Name:**	WRACWYWAPQQRKC-QZSWZRGBSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WRACWYWAPQQRKC-QZSWZRGBSA-N
Standard InCHI:	InChI=1S/C30H48O5/c1-16-10-11-30(25(34)35)13-12-28(6)18(22(30)17(16)2)8-9-21-27(5)14-20(32)24(33)26(3,4)23(27)19(31)15-29(21,28)7/h8,16-17,19-24,31-33H,9-15H2,1-7H3,(H,34,35)/p-1/t16-,17+,19-,20-,21-,22+,23+,24+,27-,28-,29-,30+/m1/s1
SMILES:	C[C@@H]1CC[C@@]2(CC[C@]3(C)C(=CC[C@@H]4[C@@]5(C)C[C@H]([C@@H](C(C)(C)[C@@H]5[C@@H](C[C@@]34C)O)O)O)[C@@H]2[C@H]1C)C(=O)[O-]
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	69569689
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

Show entries

Search:

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO20081	Mycobacterium tuberculosis	Species	Mycobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[97292]
NPO20081	Mycobacterium tuberculosis	Species	Mycobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[8917504]
NPO28011	Swertia japonica	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[5583807]
NPO20081	Mycobacterium tuberculosis	Species	Mycobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[27807341]
NPO20081	Mycobacterium tuberculosis	Species	Mycobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[27242221]
NPO28011	Swertia japonica	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26996316]
NPO28528	Bridelia ferruginea	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26938998]
NPO20081	Mycobacterium tuberculosis	Species	Mycobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[26774486]
NPO20081	Mycobacterium tuberculosis	Species	Mycobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[26466957]
NPO20081	Mycobacterium tuberculosis	Species	Mycobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[25028392]

Showing 1 to 10 of 89 entries

Previous1 2 3 4 5…9Next

☑ 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

Show entries

Search:

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

Showing 0 to 0 of 0 entries

PreviousNext

☑ 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

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
No data available in table

Showing 0 to 0 of 0 entries

PreviousNext

☑ 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 NPC278032 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	219
0.1-0.2	1376
0.2-0.3	4703
0.3-0.4	12191
0.4-0.5	10604
0.5-0.6	5547
0.6-0.7	4926
0.7-0.8	2355
0.8-0.85	422
0.85-0.9	173
0.9-0.95	146
0.95-1	35

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
No data available in table

Showing 0 to 0 of 0 entries

PreviousNext

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 NPC278032 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	195
0.1-0.2	1752
0.2-0.3	3796
0.3-0.4	2245
0.4-0.5	696
0.5-0.6	228
0.6-0.7	196
0.7-0.8	36
0.8-0.85	3
0.85-0.9	2
0.9-0.95	1
0.95-1	0

Show entries

Search:

Similarity Score	Similarity Level	Drug ID	Developmental Stage
No data available in table

Showing 0 to 0 of 0 entries

PreviousNext

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