NPASS Compound

Structure

NPC312471 OpenBabel07101718292D 34 36 0 0 1 0 0 0 0 0999 V2000 2.5000 3.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5388 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2709 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4049 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8690 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6923 -1.8035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 1.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 3.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 2.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5878 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4049 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4049 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0029 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5878 -0.8090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9511 -0.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 2.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4049 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.5388 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.5388 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.2709 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.2709 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5878 0.8090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5878 -0.8090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.0029 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9021 -0.6180 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 3.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1369 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5013 -1.2158 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1369 1.0000 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 -0.5000 1.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 8 1 0 0 0 0 2 13 1 0 0 0 0 3 13 1 0 0 0 0 4 14 2 0 0 0 0 5 15 1 0 0 0 0 6 25 1 0 0 0 0 7 26 1 0 0 0 0 8 9 1 0 0 0 0 9 18 1 0 0 0 0 10 11 1 0 0 0 0 10 17 1 0 0 0 0 11 26 1 0 0 0 0 12 25 1 0 0 0 0 14 22 1 0 0 0 0 15 27 2 0 0 0 0 15 32 1 0 0 0 0 16 12 1 6 0 0 0 16 20 1 0 0 0 0 16 33 1 0 0 0 0 17 25 1 6 0 0 0 17 28 1 0 0 0 0 18 29 2 0 0 0 0 18 34 1 0 0 0 0 19 13 1 6 0 0 0 19 21 1 0 0 0 0 19 23 1 0 0 0 0 20 14 1 1 0 0 0 20 21 1 0 0 0 0 21 24 1 0 0 0 0 22 23 1 0 0 0 0 22 30 1 0 0 0 0 23 32 1 0 0 0 0 24 26 1 0 0 0 0 24 33 1 0 0 0 0 25 31 1 0 0 0 0 26 34 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	482.29
Volume:	494.995
LogP:	2.379
LogD:	1.817
LogS:	-3.011
# Rotatable Bonds:	7
TPSA:	122.52
# H-Bond Aceptor:	8
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.404
Synthetic Accessibility Score:	6.326
Fsp3:	0.846
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:	-4.807
MDCK Permeability:	0.00010724108142312616
Pgp-inhibitor:	0.738
Pgp-substrate:	0.798
Human Intestinal Absorption (HIA):	0.038
20% Bioavailability (F20%):	0.008
30% Bioavailability (F30%):	0.556

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.029
Plasma Protein Binding (PPB):	73.72931671142578%
Volume Distribution (VD):	1.33
Pgp-substrate:	15.311616897583008%

ADMET: Metabolism

CYP1A2-inhibitor:	0.014
CYP1A2-substrate:	0.067
CYP2C19-inhibitor:	0.01
CYP2C19-substrate:	0.6
CYP2C9-inhibitor:	0.009
CYP2C9-substrate:	0.04
CYP2D6-inhibitor:	0.009
CYP2D6-substrate:	0.049
CYP3A4-inhibitor:	0.404
CYP3A4-substrate:	0.343

ADMET: Excretion

Clearance (CL):	4.083
Half-life (T1/2):	0.713

ADMET: Toxicity

hERG Blockers:	0.066
Human Hepatotoxicity (H-HT):	0.852
Drug-inuced Liver Injury (DILI):	0.663
AMES Toxicity:	0.01
Rat Oral Acute Toxicity:	0.229
Maximum Recommended Daily Dose:	0.021
Skin Sensitization:	0.087
Carcinogencity:	0.028
Eye Corrosion:	0.004
Eye Irritation:	0.012
Respiratory Toxicity:	0.505

Download Data

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

Natural Product: NPC312471

Natural Product ID:	NPC312471
*Common Name:**	QMGXMNOTQRBWAE-WOPKHISJSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QMGXMNOTQRBWAE-WOPKHISJSA-N
Standard InCHI:	InChI=1S/C26H42O8/c1-8-9-18(29)34-26(7)11-10-17(28)25(6,31)12-16-20-14(4)22(30)23(32-15(5)27)19(13(2)3)21(20)24(26)33-16/h13,16-17,19-24,28,30-31H,4,8-12H2,1-3,5-7H3/t16-,17+,19-,20-,21-,22-,23+,24-,25+,26-/m1/s1
SMILES:	CCCC(=O)O[C@]1(C)CC[C@H](O)[C@@](C[C@H]2O[C@@H]1[C@@H]1[C@@H](C(C)C)[C@H](OC(=O)C)[C@@H](C(=C)[C@H]21)O)(C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL2426315
PubChem CID:	73353797
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	=	7.35	%	PMID[540564]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	10000.0	nM	PMID[540564]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Inhibition	=	1.17	%	PMID[540564]

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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 NPC312471 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	189
0.1-0.2	1521
0.2-0.3	5110
0.3-0.4	12702
0.4-0.5	10257
0.5-0.6	7540
0.6-0.7	4938
0.7-0.8	391
0.8-0.85	19
0.85-0.9	13
0.9-0.95	11
0.95-1	6

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC471378
0.9651	High Similarity	NPC122057
0.9529	High Similarity	NPC92370
0.9529	High Similarity	NPC470260
0.9529	High Similarity	NPC75443

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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 NPC312471 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	185
0.1-0.2	2168
0.2-0.3	3841
0.3-0.4	2026
0.4-0.5	549
0.5-0.6	298
0.6-0.7	82
0.7-0.8	1
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
0.7525	Intermediate Similarity	NPD5344	Discontinued
0.7327	Intermediate Similarity	NPD4225	Approved
0.7087	Intermediate Similarity	NPD6648	Approved
0.697	Remote Similarity	NPD6698	Approved
0.697	Remote Similarity	NPD46	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