NPASS Compound

Structure

CID212699 OpenBabel06191716002D 44 47 0 0 1 0 0 0 0 0999 V2000 -0.5135 -3.9196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2149 -4.0329 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3834 2.4773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.2747 4.1779 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8379 2.7693 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9033 1.7714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9411 3.2116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0137 2.0137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0719 1.2158 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1096 2.6560 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0898 1.6310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0137 2.0137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6702 1.8939 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3103 1.3371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9917 2.8408 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6318 2.2840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0137 -3.0137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9375 -2.6310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4488 -2.4794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0081 0.1951 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3834 -3.4773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4488 1.4794 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.3296 1.1420 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1750 1.6581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9724 3.0359 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0273 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3827 0.9239 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3827 -1.9239 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.9375 1.6310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0137 -3.0137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3457 1.0372 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.3435 1.1026 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.0273 -1.0000 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 -4.6447 -1.9239 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.6447 0.9239 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.4931 2.4625 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8186 -3.9945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0081 -1.1951 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9808 -1.1951 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.2939 3.9828 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0898 -2.6310 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 1.9012 0.2057 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 21 1 0 0 0 0 2 21 1 0 0 0 0 4 41 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 6 9 1 0 0 0 0 7 10 2 0 0 0 0 8 11 1 0 0 0 0 8 12 2 0 0 0 0 9 24 2 0 0 0 0 10 24 1 0 0 0 0 11 27 1 0 0 0 0 12 29 1 0 0 0 0 13 15 1 0 0 0 0 13 23 2 0 0 0 0 14 16 2 0 0 0 0 14 23 1 0 0 0 0 15 25 2 0 0 0 0 16 25 1 0 0 0 0 17 18 1 0 0 0 0 17 30 1 0 0 0 0 18 35 1 0 0 0 0 19 21 1 0 0 0 0 20 23 1 0 0 0 0 22 3 1 6 0 0 0 25 41 1 0 0 0 0 26 20 1 1 0 0 0 26 33 1 0 0 0 0 26 36 1 0 0 0 0 27 22 1 1 0 0 0 27 43 1 0 0 0 0 28 19 1 6 0 0 0 28 34 1 0 0 0 0 28 42 1 0 0 0 0 29 36 2 3 0 0 0 29 37 1 0 0 0 0 30 38 2 0 0 0 0 30 42 1 0 0 0 0 31 22 1 6 0 0 0 31 32 1 0 0 0 0 31 44 1 0 0 0 0 32 24 1 1 0 0 0 32 44 1 0 0 0 0 33 35 2 3 0 0 0 33 39 1 0 0 0 0 34 40 2 0 0 0 0 34 43 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	606.29
Volume:	625.708
LogP:	4.438
LogD:	3.936
LogS:	-5.101
# Rotatable Bonds:	8
TPSA:	132.89
# H-Bond Aceptor:	10
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.342
Synthetic Accessibility Score:	4.99
Fsp3:	0.5
Lipinski Rule-of-5:	Accepted
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:	-5.037
MDCK Permeability:	7.711542275501415e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.013
30% Bioavailability (F30%):	0.974

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.186
Plasma Protein Binding (PPB):	94.93023681640625%
Volume Distribution (VD):	0.669
Pgp-substrate:	1.942058801651001%

ADMET: Metabolism

CYP1A2-inhibitor:	0.032
CYP1A2-substrate:	0.099
CYP2C19-inhibitor:	0.877
CYP2C19-substrate:	0.597
CYP2C9-inhibitor:	0.932
CYP2C9-substrate:	0.868
CYP2D6-inhibitor:	0.092
CYP2D6-substrate:	0.407
CYP3A4-inhibitor:	0.946
CYP3A4-substrate:	0.679

ADMET: Excretion

Clearance (CL):	6.923
Half-life (T1/2):	0.41

ADMET: Toxicity

hERG Blockers:	0.415
Human Hepatotoxicity (H-HT):	0.86
Drug-inuced Liver Injury (DILI):	0.941
AMES Toxicity:	0.062
Rat Oral Acute Toxicity:	0.691
Maximum Recommended Daily Dose:	0.272
Skin Sensitization:	0.445
Carcinogencity:	0.105
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.017

Download Data

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

Natural Product: NPC212699

Natural Product ID:	NPC212699
*Common Name:**	Arenastatin A
IUPAC Name:	(3S,10R,13E,16S)-10-[(4-methoxyphenyl)methyl]-3-(2-methylpropyl)-16-[(1S)-1-[(2R,3R)-3-phenyloxiran-2-yl]ethyl]-1,4-dioxa-8,11-diazacyclohexadec-13-ene-2,5,9,12-tetrone
Synonyms:
Standard InCHIKey:	GPUHMLPBKTYERL-DEIZWQRYSA-N
Standard InCHI:	InChI=1S/C34H42N2O8/c1-21(2)19-28-34(40)43-27(22(3)31-32(44-31)24-9-6-5-7-10-24)11-8-12-29(37)36-26(33(39)35-18-17-30(38)42-28)20-23-13-15-25(41-4)16-14-23/h5-10,12-16,21-22,26-28,31-32H,11,17-20H2,1-4H3,(H,35,39)(H,36,37)/b12-8+/t22-,26+,27-,28-,31+,32+/m0/s1
SMILES:	CC(C)C[C@H]1C(=O)O[C@@H](C/C=C/C(=N[C@H](Cc2ccc(cc2)OC)C(=NCCC(=O)O1)O)O)[C@H](C)[C@@H]1[C@@H](c2ccccc2)O1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL264224
PubChem CID:	9938734
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0001813] Peptidomimetics [CHEMONTID:0002010] Hybrid peptides

*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
NPO32667	Petrosia sp.	Species	Petrosiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[9917297]
NPO32667	Petrosia sp.	Species	Petrosiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[26821210]
NPO18618	Neurolaena lobata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24476550]
NPO32667	Petrosia sp.	Species	Petrosiidae	Eukaryota	n.a.	American Samoa	n.a.	PMID[23368996]
NPO32667	Petrosia sp.	Species	Petrosiidae	Eukaryota	n.a.	Miyako sea-knoll, southwestern Japan (2525.64' N, 12542.48' E), at a depth of 415 m	2009-OCT	PMID[21534590]
NPO18618	Neurolaena lobata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO32667	Petrosia sp.	Species	Petrosiidae	Eukaryota	n.a.	Indonesia	1996	PMID[18327911]
NPO8945	Grevillea robusta	Species	Proteaceae	Eukaryota	leaves	n.a.	n.a.	PMID[17243726]
NPO4541	Capnella lacertiliensis	Species	Nephtheidae	Eukaryota	n.a.	n.a.	n.a.	PMID[12608844]
NPO32667	Petrosia sp.	Species	Petrosiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[11754614]

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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	5
IC50	14
Others	2

Activity Type	# Activity
Cell Line	14
Individual Protein	1
Others	5
Protein Complex	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT91	Cell Line	KB	Homo sapiens	IC50	=	0.0083	nM	PMID[477645]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	88.0	nM	PMID[477644]
NPT378	Cell Line	NCI/ADR-RES	Homo sapiens	IC50	=	2400.0	nM	PMID[477644]
NPT2	Others	Unspecified	""	IC50	=	13700.0	nM	PMID[477644]
NPT2	Others	Unspecified	""	Resistance factor	=	27.3	n.a.	PMID[477644]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	130.0	nM	PMID[477643]
NPT378	Cell Line	NCI/ADR-RES	Homo sapiens	IC50	=	250.0	nM	PMID[477643]
NPT2	Others	Unspecified	""	IC50	=	15800.0	nM	PMID[477643]
NPT2	Others	Unspecified	""	Resistance factor	=	1.9	n.a.	PMID[477643]
NPT3027	Cell Line	MCF7S	Homo sapiens	IC50	=	0.13	nM	PMID[477642]

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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 NPC212699 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	193
0.1-0.2	869
0.2-0.3	3688
0.3-0.4	11402
0.4-0.5	6780
0.5-0.6	14253
0.6-0.7	5284
0.7-0.8	202
0.8-0.85	15
0.85-0.9	8
0.9-0.95	1
0.95-1	2

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC207675
0.9514	High Similarity	NPC132771
0.9	High Similarity	NPC263507
0.9	High Similarity	NPC271958
0.9	High Similarity	NPC45112

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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 NPC212699 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	132
0.1-0.2	459
0.2-0.3	1013
0.3-0.4	2077
0.4-0.5	2499
0.5-0.6	2052
0.6-0.7	856
0.7-0.8	60
0.8-0.85	0
0.85-0.9	2
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9	High Similarity	NPD7959	Clinical (unspecified phase)
0.8944	High Similarity	NPD8014	Clinical (unspecified phase)
0.8039	Intermediate Similarity	NPD7596	Clinical (unspecified phase)
0.8012	Intermediate Similarity	NPD7972	Discontinued
0.7808	Intermediate Similarity	NPD3676	Clinical (unspecified phase)

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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