NPASS Compound

Structure

NPC165218 OpenBabel07101719252D 38 43 0 0 1 0 0 0 0 0999 V2000 -1.3154 -2.1855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2339 0.4889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8780 -2.3565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8192 -0.5911 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3913 -4.9617 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5404 -0.4889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9739 1.3755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3871 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6282 0.6488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5404 2.4445 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9520 -2.8986 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1829 0.0054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7266 -0.6543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9095 -1.4090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0807 0.9778 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6936 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5404 1.4667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6435 -1.4453 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6499 -3.8285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3871 2.9333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6936 0.9778 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.9778 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8468 1.4667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2339 1.4667 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5645 -0.3798 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3871 0.9778 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3289 -1.5475 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8468 -0.4889 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.8791 -1.5352 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3041 -4.5551 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3871 3.9111 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8468 2.4445 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5747 0.7910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6935 -4.0318 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1393 -0.1979 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5341 -0.5061 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2339 2.4445 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 14 1 0 0 0 0 4 28 1 0 0 0 0 5 35 1 0 0 0 0 6 8 1 0 0 0 0 6 16 1 0 0 0 0 7 9 2 0 0 0 0 7 15 1 0 0 0 0 8 26 1 0 0 0 0 9 36 1 0 0 0 0 10 17 1 0 0 0 0 10 20 1 0 0 0 0 11 18 1 0 0 0 0 11 19 1 0 0 0 0 12 15 2 0 0 0 0 12 36 1 0 0 0 0 13 27 1 0 0 0 0 13 29 1 0 0 0 0 14 30 2 0 0 0 0 14 37 1 0 0 0 0 15 24 1 0 0 0 0 16 21 1 0 0 0 0 16 28 1 1 0 0 0 17 21 2 0 0 0 0 17 26 1 0 0 0 0 18 27 1 6 0 0 0 18 28 1 0 0 0 0 19 31 2 0 0 0 0 19 35 1 0 0 0 0 20 32 2 0 0 0 0 20 38 1 0 0 0 0 21 23 1 0 0 0 0 22 23 1 0 0 0 0 22 25 1 0 0 0 0 22 29 1 6 0 0 0 23 33 2 0 0 0 0 24 26 1 6 0 0 0 24 38 1 0 0 0 0 25 27 1 6 0 0 0 25 37 1 0 0 0 0 26 2 1 6 0 0 0 27 3 1 6 0 0 0 28 29 1 6 0 0 0 29 34 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	526.22
Volume:	519.458
LogP:	2.868
LogD:	1.652
LogS:	-4.612
# Rotatable Bonds:	6
TPSA:	129.34
# H-Bond Aceptor:	9
# H-Bond Donor:	1
# Rings:	6
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.463
Synthetic Accessibility Score:	6.08
Fsp3:	0.655
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-5.362
MDCK Permeability:	2.3533419152954593e-05
Pgp-inhibitor:	0.995
Pgp-substrate:	0.245
Human Intestinal Absorption (HIA):	0.114
20% Bioavailability (F20%):	0.991
30% Bioavailability (F30%):	0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.835
Plasma Protein Binding (PPB):	80.3098373413086%
Volume Distribution (VD):	0.601
Pgp-substrate:	18.431161880493164%

ADMET: Metabolism

CYP1A2-inhibitor:	0.016
CYP1A2-substrate:	0.118
CYP2C19-inhibitor:	0.279
CYP2C19-substrate:	0.113
CYP2C9-inhibitor:	0.302
CYP2C9-substrate:	0.022
CYP2D6-inhibitor:	0.016
CYP2D6-substrate:	0.055
CYP3A4-inhibitor:	0.948
CYP3A4-substrate:	0.39

ADMET: Excretion

Clearance (CL):	3.951
Half-life (T1/2):	0.606

ADMET: Toxicity

hERG Blockers:	0.056
Human Hepatotoxicity (H-HT):	0.4
Drug-inuced Liver Injury (DILI):	0.334
AMES Toxicity:	0.034
Rat Oral Acute Toxicity:	0.988
Maximum Recommended Daily Dose:	0.693
Skin Sensitization:	0.217
Carcinogencity:	0.794
Eye Corrosion:	0.012
Eye Irritation:	0.019
Respiratory Toxicity:	0.988

Download Data

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

Natural Product: NPC165218

Natural Product ID:	NPC165218
*Common Name:**	Moluccensin J
IUPAC Name:	n.a.
Synonyms:	Moluccensin J
Standard InCHIKey:	LSBZEHLCUALPOF-GBPDNJNKSA-N
Standard InCHI:	InChI=1S/C29H34O9/c1-14(30)37-25-22-23(33)21-16(28(4)18(11-19(31)35-5)27(25,3)13-29(22,28)34)6-8-26(2)17(21)10-20(32)38-24(26)15-7-9-36-12-15/h7,9,12,16,18,22,24-25,34H,6,8,10-11,13H2,1-5H3/t16-,18-,22-,24-,25+,26+,27-,28+,29-/m0/s1
SMILES:	CC(=O)O[C@@H]1[C@@H]2C(=O)C3=C4CC(=O)O[C@@H](c5ccoc5)[C@]4(C)CC[C@@H]3[C@]3(C)[C@@H](CC(=O)OC)[C@]1(C)C[C@]23O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1087404
PubChem CID:	46184329
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids [CHEMONTID:0002380] Limonoids

*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
NPO6445	Xylocarpus moluccensis	Species	Meliaceae	Eukaryota	seeds	n.a.	n.a.	PMID[26114936]
NPO6445	Xylocarpus moluccensis	Species	Meliaceae	Eukaryota	seeds	n.a.	n.a.	PMID[22724531]
NPO6445	Xylocarpus moluccensis	Species	Meliaceae	Eukaryota	seeds	Thai	n.a.	PMID[21733687]
NPO6445	Xylocarpus moluccensis	Species	Meliaceae	Eukaryota	seeds	n.a.	n.a.	PMID[20146503]
NPO6445	Xylocarpus moluccensis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20112995]
NPO6445	Xylocarpus moluccensis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

Showing 1 to 6 of 6 entries

Previous1Next

☑ 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

Activity Type	# Activity
IC50	5

Activity Type	# Activity
Cell Line	3
NON-MOLECULAR	2

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT845	Cell Line	BT-474	Homo sapiens	IC50	>	10.0	ug.mL-1	PMID[532201]
NPT65	Cell Line	HepG2	Homo sapiens	IC50	>	10.0	ug.mL-1	PMID[532201]
NPT323	Cell Line	SW-620	Homo sapiens	IC50	>	10.0	ug.mL-1	PMID[532201]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	10.0	ug.mL-1	PMID[532201]

Showing 1 to 4 of 4 entries

Previous1Next

☑ 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 NPC165218 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	355
0.1-0.2	1460
0.2-0.3	3066
0.3-0.4	5503
0.4-0.5	10781
0.5-0.6	10661
0.6-0.7	9340
0.7-0.8	1062
0.8-0.85	342
0.85-0.9	110
0.9-0.95	13
0.95-1	4

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
0.9615	High Similarity	NPC478178
0.95	High Similarity	NPC94763
0.95	High Similarity	NPC236004
0.9308	High Similarity	NPC478179
0.9299	High Similarity	NPC472767

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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 NPC165218 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	302
0.1-0.2	998
0.2-0.3	2193
0.3-0.4	2694
0.4-0.5	1875
0.5-0.6	812
0.6-0.7	262
0.7-0.8	12
0.8-0.85	0
0.85-0.9	2
0.9-0.95	0
0.95-1	0

Show entries

Search:

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9103	High Similarity	NPD5761	Phase 2
0.9103	High Similarity	NPD5760	Phase 2
0.7976	Intermediate Similarity	NPD5537	Clinical (unspecified phase)
0.7966	Intermediate Similarity	NPD8434	Phase 2
0.7886	Intermediate Similarity	NPD6764	Approved

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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