NPASS Compound

Structure

NPC170286 OpenBabel07101718182D 28 30 0 0 1 0 0 0 0 0999 V2000 2.7600 -2.3174 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4469 3.5761 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0807 2.6201 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6631 -3.7035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0917 -0.8209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2658 -1.8565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5932 2.5125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4592 2.0125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2686 -1.7818 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0151 1.4888 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3098 0.5333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8768 -0.7581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1966 -1.4912 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5960 2.5872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9169 1.6336 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9829 -2.9704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0225 1.1863 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3349 2.2219 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.1716 0.1974 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5975 -1.2818 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.6187 0.9212 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1608 -0.4556 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0080 -3.1930 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6075 1.0702 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2776 -2.0149 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1581 0.0336 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3676 1.1916 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 1 13 1 0 0 0 0 2 14 1 0 0 0 0 3 15 2 0 0 0 0 4 16 1 0 0 0 0 6 9 1 0 0 0 0 6 13 1 0 0 0 0 7 8 1 0 0 0 0 7 14 2 0 0 0 0 9 20 1 0 0 0 0 10 11 1 0 0 0 0 11 22 1 0 0 0 0 12 13 2 0 0 0 0 14 18 1 0 0 0 0 15 17 1 0 0 0 0 15 21 1 0 0 0 0 16 23 2 0 0 0 0 16 25 1 0 0 0 0 17 8 1 1 0 0 0 17 19 1 0 0 0 0 18 10 1 1 0 0 0 18 27 1 0 0 0 0 19 12 1 1 0 0 0 19 26 1 0 0 0 0 20 22 1 6 0 0 0 20 25 1 0 0 0 0 21 24 2 0 0 0 0 21 26 1 0 0 0 0 22 5 1 6 0 0 0 22 28 1 0 0 0 0 27 28 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	390.2
Volume:	402.958
LogP:	3.234
LogD:	2.952
LogS:	-4.256
# Rotatable Bonds:	2
TPSA:	71.06
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.292
Synthetic Accessibility Score:	5.891
Fsp3:	0.636
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	3
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.709
MDCK Permeability:	4.288586933398619e-05
Pgp-inhibitor:	0.358
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.759
20% Bioavailability (F20%):	0.737
30% Bioavailability (F30%):	0.914

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.219
Plasma Protein Binding (PPB):	90.11698150634766%
Volume Distribution (VD):	1.582
Pgp-substrate:	6.100572109222412%

ADMET: Metabolism

CYP1A2-inhibitor:	0.069
CYP1A2-substrate:	0.115
CYP2C19-inhibitor:	0.186
CYP2C19-substrate:	0.44
CYP2C9-inhibitor:	0.314
CYP2C9-substrate:	0.12
CYP2D6-inhibitor:	0.112
CYP2D6-substrate:	0.769
CYP3A4-inhibitor:	0.649
CYP3A4-substrate:	0.313

ADMET: Excretion

Clearance (CL):	4.427
Half-life (T1/2):	0.344

ADMET: Toxicity

hERG Blockers:	0.028
Human Hepatotoxicity (H-HT):	0.743
Drug-inuced Liver Injury (DILI):	0.835
AMES Toxicity:	0.792
Rat Oral Acute Toxicity:	0.503
Maximum Recommended Daily Dose:	0.904
Skin Sensitization:	0.895
Carcinogencity:	0.16
Eye Corrosion:	0.236
Eye Irritation:	0.035
Respiratory Toxicity:	0.967

Download Data

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

Natural Product: NPC170286

Natural Product ID:	NPC170286
*Common Name:**	Denticulatolide
IUPAC Name:	n.a.
Synonyms:	Denticulatolide
Standard InCHIKey:	DCNHEHMOEMETOF-SNTVFBAHSA-N
Standard InCHI:	InChI=1S/C22H30O6/c1-13-6-9-20(25-16(4)23)22(5)11-10-18(27-28-22)14(2)7-8-17-15(3)21(24)26-19(17)12-13/h7,12,17-20H,3,6,8-11H2,1-2,4-5H3/b13-12+,14-7-/t17-,18-,19-,20-,22+/m0/s1
SMILES:	C/C/1=C[C@H]2[C@@H](C/C=C(/C)[C@@H]3CC[C@](C)([C@H](CC1)OC(=O)C)OO3)C(=C)C(=O)O2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL485788
PubChem CID:	10430489
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000147] Macrolides and analogues

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO27251	Lobophytum crassum	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[9548852]
NPO9909	Sarcophyton crassocaule	Species	Alcyoniidae	Eukaryota	n.a.	Formosan soft coral	n.a.	PMID[22014827]
NPO27251	Lobophytum crassum	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[18973388]
NPO27251	Lobophytum crassum	Species	Alcyoniidae	Eukaryota	n.a.	south china sea	n.a.	PMID[18512986]
NPO9909	Sarcophyton crassocaule	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[17125220]
NPO9909	Sarcophyton crassocaule	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[17067165]
NPO9909	Sarcophyton crassocaule	Species	Alcyoniidae	Eukaryota	n.a.	formosan soft coral	n.a.	PMID[11141104]
NPO9909	Sarcophyton crassocaule	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27251	Lobophytum crassum	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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☑ 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

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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

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☑ 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
ED50	4
IC50	6
Others	2

Activity Type	# Activity
Cell Line	11
NON-MOLECULAR	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT65	Cell Line	HepG2	Homo sapiens	IC50	=	2.4	ug.mL-1	PMID[448657]
NPT82	Cell Line	MDA-MB-231	Homo sapiens	IC50	=	2.0	ug.mL-1	PMID[448657]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	2.0	ug.mL-1	PMID[448657]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	2.3	ug.mL-1	PMID[448657]
NPT1031	Cell Line	Ca9-22	Homo sapiens	IC50	=	1.2	ug.mL-1	PMID[448657]
NPT113	Cell Line	RAW264.7	Mus musculus	Activity	=	10.2	%	PMID[448657]
NPT113	Cell Line	RAW264.7	Mus musculus	Activity	=	34.3	%	PMID[448657]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	2.5	ug.mL-1	PMID[448657]
NPT81	Cell Line	A549	Homo sapiens	ED50	=	6.46	ug ml-1	PMID[448656]
NPT139	Cell Line	HT-29	Homo sapiens	ED50	=	5.78	ug ml-1	PMID[448656]

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☑ 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 NPC170286 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	169
0.1-0.2	1085
0.2-0.3	4779
0.3-0.4	12080
0.4-0.5	11559
0.5-0.6	7744
0.6-0.7	4258
0.7-0.8	998
0.8-0.85	24
0.85-0.9	0
0.9-0.95	0
0.95-1	1

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Similarity Score	Similarity Level	Natural Product ID
0.881	High Similarity	NPC231889
0.8506	High Similarity	NPC475748
0.8506	High Similarity	NPC51004
0.8471	Intermediate Similarity	NPC50637
0.8409	Intermediate Similarity	NPC30515

Showing 1 to 5 of 200 entries

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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 NPC170286 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	152
0.1-0.2	1380
0.2-0.3	4043
0.3-0.4	2442
0.4-0.5	733
0.5-0.6	314
0.6-0.7	79
0.7-0.8	7
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.814	Intermediate Similarity	NPD1733	Clinical (unspecified phase)
0.7889	Intermediate Similarity	NPD6698	Approved
0.7889	Intermediate Similarity	NPD46	Approved
0.7684	Intermediate Similarity	NPD8029	Clinical (unspecified phase)
0.7582	Intermediate Similarity	NPD1695	Approved

Showing 1 to 5 of 165 entries

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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