NPASS Compound

Structure

NPC246347 OpenBabel07101719152D 40 42 0 0 1 0 0 0 0 0999 V2000 0.8660 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0012 -0.7421 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -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 -3.4049 -3.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0972 0.8035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9049 -2.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3559 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9927 -1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4049 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0501 -1.0511 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 -2.4049 -3.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8171 -0.1910 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3559 -0.6910 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 -2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8171 -1.8090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9927 -0.1910 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4049 -2.0000 0.0000 C 0 0 1 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 1.7321 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -4.8422 -2.0292 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9049 -4.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9062 0.2158 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 0.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3070 -0.3820 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 O 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 -2.4049 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9049 -2.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 13 1 0 0 0 0 2 13 1 0 0 0 0 3 14 1 0 0 0 0 4 15 1 0 0 0 0 5 16 1 0 0 0 0 6 17 1 0 0 0 0 7 26 1 0 0 0 0 8 27 1 0 0 0 0 9 10 1 0 0 0 0 9 19 1 0 0 0 0 10 27 1 0 0 0 0 11 26 1 0 0 0 0 12 28 1 0 0 0 0 12 29 1 0 0 0 0 14 30 2 0 0 0 0 14 36 1 0 0 0 0 15 31 2 0 0 0 0 15 37 1 0 0 0 0 16 32 2 0 0 0 0 16 38 1 0 0 0 0 17 33 2 0 0 0 0 17 40 1 0 0 0 0 18 11 1 6 0 0 0 18 22 1 0 0 0 0 18 39 1 0 0 0 0 19 26 1 6 0 0 0 19 36 1 0 0 0 0 20 13 1 6 0 0 0 20 21 1 0 0 0 0 20 23 1 0 0 0 0 21 22 1 0 0 0 0 21 24 1 0 0 0 0 22 28 1 0 0 0 0 23 25 1 0 0 0 0 23 37 1 0 0 0 0 24 27 1 0 0 0 0 24 39 1 0 0 0 0 25 28 1 0 0 0 0 25 38 1 0 0 0 0 26 34 1 0 0 0 0 27 40 1 0 0 0 0 28 35 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	590.25
Volume:	568.532
LogP:	2.722
LogD:	1.326
LogS:	-2.989
# Rotatable Bonds:	10
TPSA:	154.89
# H-Bond Aceptor:	11
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.266
Synthetic Accessibility Score:	6.446
Fsp3:	0.857
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.275
MDCK Permeability:	0.00011836663907160982
Pgp-inhibitor:	0.989
Pgp-substrate:	0.007
Human Intestinal Absorption (HIA):	0.195
20% Bioavailability (F20%):	0.02
30% Bioavailability (F30%):	0.914

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.294
Plasma Protein Binding (PPB):	52.43738555908203%
Volume Distribution (VD):	1.451
Pgp-substrate:	24.000137329101562%

ADMET: Metabolism

CYP1A2-inhibitor:	0.011
CYP1A2-substrate:	0.027
CYP2C19-inhibitor:	0.008
CYP2C19-substrate:	0.188
CYP2C9-inhibitor:	0.004
CYP2C9-substrate:	0.015
CYP2D6-inhibitor:	0.23
CYP2D6-substrate:	0.046
CYP3A4-inhibitor:	0.321
CYP3A4-substrate:	0.353

ADMET: Excretion

Clearance (CL):	2.354
Half-life (T1/2):	0.816

ADMET: Toxicity

hERG Blockers:	0.025
Human Hepatotoxicity (H-HT):	0.958
Drug-inuced Liver Injury (DILI):	0.872
AMES Toxicity:	0.071
Rat Oral Acute Toxicity:	0.079
Maximum Recommended Daily Dose:	0.012
Skin Sensitization:	0.569
Carcinogencity:	0.118
Eye Corrosion:	0.102
Eye Irritation:	0.027
Respiratory Toxicity:	0.031

Download Data

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

Natural Product: NPC246347

Natural Product ID:	NPC246347
*Common Name:**	YMBPQCOCUHBPTR-SEQDWNMISA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YMBPQCOCUHBPTR-SEQDWNMISA-N
Standard InCHI:	InChI=1S/C28H43ClO11/c1-13(2)20-21-22(28(35,12-29)25(38-16(5)32)23(20)37-15(4)31)18-11-26(7,34)19(36-14(3)30)9-10-27(8,24(21)39-18)40-17(6)33/h13,18-25,34-35H,9-12H2,1-8H3/t18-,19+,20-,21-,22-,23+,24-,25+,26+,27-,28-/m1/s1
SMILES:	CC(C)[C@@H]1[C@@H]2[C@@H]([C@H]3C[C@@](C)([C@H](CC[C@](C)([C@@H]2O3)OC(=O)C)OC(=O)C)O)[C@](CCl)([C@H]([C@H]1OC(=O)C)OC(=O)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL2426308
PubChem CID:	73350842
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0002916] Eunicellane and asbestinane diterpenoids

*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
NPO16055	Klyxum molle	Species	Alcyoniidae	Eukaryota	n.a.	Formosan soft coral	n.a.	PMID[24020806]
NPO16055	Klyxum molle	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[22004052]
NPO16055	Klyxum molle	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
IC50	2
Others	2

Activity Type	# Activity
NON-MOLECULAR	4

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Inhibition	=	6.42	%	PMID[533012]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	10000.0	nM	PMID[533012]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Inhibition	=	9.36	%	PMID[533012]

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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 NPC246347 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	413
0.1-0.2	4001
0.2-0.3	12495
0.3-0.4	12976
0.4-0.5	8039
0.5-0.6	4325
0.6-0.7	376
0.7-0.8	56
0.8-0.85	6
0.85-0.9	6
0.9-0.95	0
0.95-1	4

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Similarity Score	Similarity Level	Natural Product ID
0.9877	High Similarity	NPC471377
0.9875	High Similarity	NPC93616
0.9753	High Similarity	NPC279260
0.878	High Similarity	NPC186594
0.8765	High Similarity	NPC43463

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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 NPC246347 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	424
0.1-0.2	4148
0.2-0.3	3219
0.3-0.4	832
0.4-0.5	429
0.5-0.6	96
0.6-0.7	2
0.7-0.8	0
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
0.7059	Intermediate Similarity	NPD7532	Clinical (unspecified phase)
0.6747	Remote Similarity	NPD371	Approved
0.6354	Remote Similarity	NPD3670	Clinical (unspecified phase)
0.6354	Remote Similarity	NPD3669	Approved
0.6168	Remote Similarity	NPD1700	Approved

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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