NPASS Compound

Structure

NPC150014 OpenBabel06302215422D 42 45 0 0 1 0 0 0 0 0999 V2000 -1.2500 -4.2270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2500 -4.2270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2500 -3.3610 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2500 -2.4950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2500 -1.6290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2500 -0.7629 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -1.2500 -0.7629 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2500 0.1031 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.2500 0.1031 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7500 0.9691 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.2500 1.8351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2500 1.8351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2500 0.9691 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.2500 0.1031 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.2500 -0.7629 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2500 -1.6290 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2500 -0.7629 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7500 0.1031 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7500 0.1031 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2500 0.9691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7500 1.8351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7500 1.8351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2500 2.7012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7500 3.5672 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7500 3.5672 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2500 2.7012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2500 4.4332 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7500 5.2993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2500 4.4332 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2500 0.9691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2500 0.1031 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7500 -0.7629 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2500 -1.6290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7500 -2.4950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7500 -2.4950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2500 -1.6290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7500 -0.7629 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2500 -1.6290 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7500 -0.7629 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2500 -3.3610 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7500 2.7012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2500 -5.0931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 42 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 8 6 1 6 0 0 0 8 9 1 0 0 0 0 8 13 1 0 0 0 0 9 10 1 0 0 0 0 10 31 1 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 41 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 6 0 0 0 14 31 1 0 0 0 0 15 16 2 0 0 0 0 15 17 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 18 30 1 0 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 21 26 2 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 29 1 0 0 0 0 25 26 1 0 0 0 0 25 27 1 0 0 0 0 27 28 1 0 0 0 0 31 32 1 1 0 0 0 32 37 2 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 34 35 1 0 0 0 0 35 36 2 0 0 0 0 35 40 1 0 0 0 0 36 37 1 0 0 0 0 36 38 1 0 0 0 0 38 39 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	572.31
Volume:	620.726
LogP:	6.591
LogD:	4.939
LogS:	-4.84
# Rotatable Bonds:	12
TPSA:	93.06
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.154
Synthetic Accessibility Score:	5.333
Fsp3:	0.444
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	2
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.79
MDCK Permeability:	1.4069099961488973e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.02
Human Intestinal Absorption (HIA):	0.411
20% Bioavailability (F20%):	0.584
30% Bioavailability (F30%):	0.493

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.017
Plasma Protein Binding (PPB):	98.38629150390625%
Volume Distribution (VD):	2.44
Pgp-substrate:	2.281057357788086%

ADMET: Metabolism

CYP1A2-inhibitor:	0.083
CYP1A2-substrate:	0.953
CYP2C19-inhibitor:	0.907
CYP2C19-substrate:	0.778
CYP2C9-inhibitor:	0.911
CYP2C9-substrate:	0.972
CYP2D6-inhibitor:	0.455
CYP2D6-substrate:	0.868
CYP3A4-inhibitor:	0.862
CYP3A4-substrate:	0.851

ADMET: Excretion

Clearance (CL):	16.101
Half-life (T1/2):	0.452

ADMET: Toxicity

hERG Blockers:	0.438
Human Hepatotoxicity (H-HT):	0.687
Drug-inuced Liver Injury (DILI):	0.759
AMES Toxicity:	0.015
Rat Oral Acute Toxicity:	0.508
Maximum Recommended Daily Dose:	0.806
Skin Sensitization:	0.611
Carcinogencity:	0.049
Eye Corrosion:	0.003
Eye Irritation:	0.021
Respiratory Toxicity:	0.955

Download Data

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

Natural Product: NPC150014

Natural Product ID:	NPC150014
*Common Name:**	NWEYCPRNIYPLIB-YCIFWMGRSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NWEYCPRNIYPLIB-YCIFWMGRSA-N
Standard InCHI:	InChI=1S/C36H44O6/c1-21(2)8-7-9-22(3)27-20-28-23(4)16-29(27)36(35(28)25-12-15-31(39)34(18-25)42-6)32(40)19-26(37)13-10-24-11-14-30(38)33(17-24)41-5/h8,10-19,22,27-29,35-39H,7,9,20H2,1-6H3/b13-10+,26-19-/t22?,27-,28?,29?,35-,36+/m1/s1
SMILES:	CC(=CCCC(C)[C@H]1CC2C(=CC1[C@@H](C(=O)/C=C(/C=C/c1ccc(c(c1)OC)O)O)[C@@H]2c1ccc(c(c1)OC)O)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	102230689
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002650] Diarylheptanoids [CHEMONTID:0002651] Linear diarylheptanoids

*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
NPO24124	Curcuma longa	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9584408]
NPO24124	Curcuma longa	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28068085]
NPO24124	Curcuma longa	Species	Zingiberaceae	Eukaryota	n.a.	leaf	n.a.	PMID[23901173]
NPO24124	Curcuma longa	Species	Zingiberaceae	Eukaryota	Rhizomes	n.a.	n.a.	PMID[23153397]
NPO24124	Curcuma longa	Species	Zingiberaceae	Eukaryota	rhizome	n.a.	n.a.	PMID[12617587]
NPO24124	Curcuma longa	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12350137]
NPO24124	Curcuma longa	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24124	Curcuma longa	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO24124	Curcuma longa	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24124	Curcuma longa	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]

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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

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
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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 NPC150014 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	352
0.1-0.2	1408
0.2-0.3	2722
0.3-0.4	7803
0.4-0.5	11035
0.5-0.6	4154
0.6-0.7	9804
0.7-0.8	5181
0.8-0.85	185
0.85-0.9	51
0.9-0.95	2
0.95-1	0

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Similarity Score	Similarity Level	Natural Product ID
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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 NPC150014 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	315
0.1-0.2	906
0.2-0.3	1308
0.3-0.4	2477
0.4-0.5	2210
0.5-0.6	1140
0.6-0.7	690
0.7-0.8	101
0.8-0.85	3
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
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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