NPASS Compound

Structure

CID55462 OpenBabel06191715392D 32 35 0 0 1 0 0 0 0 0999 V2000 -5.0013 -0.7052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8689 -1.9622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6590 -5.1850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3861 -3.9431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8465 -2.4785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6009 -5.3885 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7772 -3.7067 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5387 -0.4879 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6922 0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0774 -2.9298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0771 -1.9531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6930 -2.9308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8454 -1.4662 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5395 -3.4192 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0006 -1.9546 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3465 -0.3530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0722 -1.0068 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2326 -4.3950 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5390 -1.4652 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2323 -3.4187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3855 -1.9536 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6927 -1.9541 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8459 -0.4884 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8457 -0.4889 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4174 -0.6545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3858 -2.9303 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8462 -1.4657 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6917 -0.0007 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 5.2035 -4.4967 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.2141 -1.6099 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 17 1 0 0 0 0 2 17 1 0 0 0 0 6 30 1 0 0 0 0 7 30 1 0 0 0 0 8 9 1 0 0 0 0 9 23 1 0 0 0 0 10 11 1 0 0 0 0 10 20 2 0 0 0 0 11 21 1 0 0 0 0 12 14 1 0 0 0 0 12 22 1 0 0 0 0 13 15 1 0 0 0 0 13 24 1 0 0 0 0 14 27 1 0 0 0 0 15 28 1 0 0 0 0 16 17 2 0 0 0 0 16 25 1 0 0 0 0 18 3 1 1 0 0 0 18 20 1 0 0 0 0 18 30 1 0 0 0 0 19 8 1 1 0 0 0 19 21 1 0 0 0 0 19 22 1 0 0 0 0 20 27 1 0 0 0 0 21 27 1 6 0 0 0 22 28 1 6 0 0 0 23 26 1 0 0 0 0 23 28 1 6 0 0 0 24 26 1 0 0 0 0 24 29 1 6 0 0 0 25 29 2 3 0 0 0 25 31 1 0 0 0 0 26 32 1 6 0 0 0 27 4 1 6 0 0 0 28 5 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	442.36
Volume:	490.283
LogP:	4.949
LogD:	4.637
LogS:	-4.84
# Rotatable Bonds:	5
TPSA:	52.57
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.479
Synthetic Accessibility Score:	4.83
Fsp3:	0.821
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.875
MDCK Permeability:	1.0987075256707612e-05
Pgp-inhibitor:	0.991
Pgp-substrate:	0.602
Human Intestinal Absorption (HIA):	0.018
20% Bioavailability (F20%):	0.238
30% Bioavailability (F30%):	0.088

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.189
Plasma Protein Binding (PPB):	69.10240936279297%
Volume Distribution (VD):	0.882
Pgp-substrate:	25.31585121154785%

ADMET: Metabolism

CYP1A2-inhibitor:	0.111
CYP1A2-substrate:	0.865
CYP2C19-inhibitor:	0.403
CYP2C19-substrate:	0.938
CYP2C9-inhibitor:	0.305
CYP2C9-substrate:	0.123
CYP2D6-inhibitor:	0.409
CYP2D6-substrate:	0.899
CYP3A4-inhibitor:	0.897
CYP3A4-substrate:	0.645

ADMET: Excretion

Clearance (CL):	9.012
Half-life (T1/2):	0.155

ADMET: Toxicity

hERG Blockers:	0.051
Human Hepatotoxicity (H-HT):	0.374
Drug-inuced Liver Injury (DILI):	0.126
AMES Toxicity:	0.005
Rat Oral Acute Toxicity:	0.941
Maximum Recommended Daily Dose:	0.912
Skin Sensitization:	0.728
Carcinogencity:	0.518
Eye Corrosion:	0.323
Eye Irritation:	0.074
Respiratory Toxicity:	0.984

Download Data

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

Natural Product: NPC55462

Natural Product ID:	NPC55462
*Common Name:**	Hookerianamide J
IUPAC Name:	N-[(3S,4R,5R,8R,9S,10R,13S,14S)-17-[(1S)-1-(dimethylamino)ethyl]-4-hydroxy-10,13-dimethyl-2,3,4,5,6,7,8,9,11,12,14,15-dodecahydro-1H-cyclopenta[a]phenanthren-3-yl]-3-methylbut-2-enamide
Synonyms:	hookerianamide J
Standard InCHIKey:	UBWMSSICUOCSHT-BJHCZKLTSA-N
Standard InCHI:	InChI=1S/C28H46N2O2/c1-17(2)16-25(31)29-24-13-15-28(5)22-12-14-27(4)20(18(3)30(6)7)10-11-21(27)19(22)8-9-23(28)26(24)32/h10,16,18-19,21-24,26,32H,8-9,11-15H2,1-7H3,(H,29,31)/t18-,19-,21-,22-,23-,24-,26+,27+,28+/m0/s1
SMILES:	CC(=CC(=N[C@H]1CC[C@]2(C)[C@H]3CC[C@]4(C)C(=CC[C@H]4[C@@H]3CC[C@H]2[C@H]1O)[C@H](C)N(C)C)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL496487
PubChem CID:	25016666
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001295] Hydroxysteroids

*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
NPO6711	Streptomyces mirabilis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19818612]
NPO12900	Sarcococca hookeriana	Species	Buxaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[18681480]
NPO12900	Sarcococca hookeriana	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18681480]
NPO12900	Sarcococca hookeriana	Species	Buxaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[17827771]
NPO5033	Alpinia galanga	Species	Zingiberaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[15930771]
NPO5033	Alpinia galanga	Species	Zingiberaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[12951092]
NPO5033	Alpinia galanga	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12951092]
NPO2332	Plantago serraria	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10911	Euphorbia peplis	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13128	Crotalaria rosenii	Species	Fabaceae	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	3
MIC	2
Others	2

Activity Type	# Activity
Individual Protein	2
Organism	5

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT204	Individual Protein	Acetylcholinesterase	Homo sapiens	IC50	=	48500.0	nM	PMID[459759]
NPT439	Individual Protein	Butyrylcholinesterase	Homo sapiens	IC50	=	800.0	nM	PMID[459759]
NPT841	Organism	Leishmania major	Leishmania major	IC50	=	11300.0	nM	PMID[459759]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	IZ	=	15.0	mm	PMID[459759]
NPT2921	Organism	Pseudomonas	Pseudomonas	IZ	=	12.0	mm	PMID[459759]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	=	141400.0	nM	PMID[459759]
NPT2921	Organism	Pseudomonas	Pseudomonas	MIC	=	70700.0	nM	PMID[459759]

Showing 1 to 7 of 7 entries

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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 NPC55462 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	92
0.1-0.2	774
0.2-0.3	7754
0.3-0.4	18687
0.4-0.5	10244
0.5-0.6	4469
0.6-0.7	631
0.7-0.8	35
0.8-0.85	5
0.85-0.9	2
0.9-0.95	3
0.95-1	1

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Similarity Score	Similarity Level	Natural Product ID
0.9223	High Similarity	NPC472359
0.91	High Similarity	NPC471083
0.9048	High Similarity	NPC469968
0.9048	High Similarity	NPC80834
0.8911	High Similarity	NPC247060

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 NPC55462 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	93
0.1-0.2	387
0.2-0.3	2545
0.3-0.4	4329
0.4-0.5	1492
0.5-0.6	285
0.6-0.7	18
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
0.7692	Intermediate Similarity	NPD5771	Approved
0.6765	Remote Similarity	NPD7525	Registered
0.6727	Remote Similarity	NPD5769	Clinical (unspecified phase)
0.6441	Remote Similarity	NPD6640	Phase 3
0.6436	Remote Similarity	NPD6942	Approved

Showing 1 to 5 of 112 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