NPASS Compound

Structure

NPC204341 OpenBabel07101718292D 33 36 0 0 1 0 0 0 0 0999 V2000 2.3039 2.5474 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7791 3.2790 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4287 4.9274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1777 1.4283 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5279 -0.4865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3786 2.8481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6852 -2.9189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8426 -2.4324 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4973 -0.4865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9254 -1.2736 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0761 2.6721 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2131 -1.4595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6852 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3705 -0.9730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2246 3.5975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8426 0.4865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3705 -2.9189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1280 4.0021 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2260 1.2260 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5279 -2.4324 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2131 -2.4324 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8426 -1.4595 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9254 0.3007 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6852 -0.9730 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 -0.9730 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3957 0.8889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5279 -1.4595 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.1763 3.7998 0.0000 C 0 0 1 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 -5.0557 -2.9189 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1762 1.6760 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3634 0.9906 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9740 4.7515 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 1 0 0 0 0 2 18 2 0 0 0 0 3 18 1 0 0 0 0 6 28 1 0 0 0 0 7 8 2 0 0 0 0 7 20 1 0 0 0 0 9 10 1 0 0 0 0 9 23 1 0 0 0 0 10 25 1 0 0 0 0 11 15 1 0 0 0 0 11 19 1 0 0 0 0 12 14 2 0 0 0 0 12 21 1 0 0 0 0 13 16 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 29 1 0 0 0 0 17 20 2 0 0 0 0 17 21 1 0 0 0 0 18 28 1 0 0 0 0 19 4 1 1 0 0 0 19 23 1 0 0 0 0 20 27 1 0 0 0 0 21 30 2 0 0 0 0 22 8 1 6 0 0 0 22 24 1 0 0 0 0 22 25 1 0 0 0 0 23 29 1 1 0 0 0 24 27 1 1 0 0 0 25 29 1 1 0 0 0 26 31 2 0 0 0 0 26 32 1 0 0 0 0 27 5 1 1 0 0 0 28 33 1 6 0 0 0 29 26 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	452.29
Volume:	495.256
LogP:	4.379
LogD:	3.829
LogS:	-4.598
# Rotatable Bonds:	7
TPSA:	74.6
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.463
Synthetic Accessibility Score:	5.167
Fsp3:	0.655
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:	-5.205
MDCK Permeability:	2.318785664101597e-05
Pgp-inhibitor:	0.072
Pgp-substrate:	0.101
Human Intestinal Absorption (HIA):	0.115
20% Bioavailability (F20%):	0.008
30% Bioavailability (F30%):	0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.962
Plasma Protein Binding (PPB):	92.0995101928711%
Volume Distribution (VD):	0.384
Pgp-substrate:	7.1471266746521%

ADMET: Metabolism

CYP1A2-inhibitor:	0.01
CYP1A2-substrate:	0.374
CYP2C19-inhibitor:	0.035
CYP2C19-substrate:	0.697
CYP2C9-inhibitor:	0.207
CYP2C9-substrate:	0.068
CYP2D6-inhibitor:	0.013
CYP2D6-substrate:	0.062
CYP3A4-inhibitor:	0.324
CYP3A4-substrate:	0.89

ADMET: Excretion

Clearance (CL):	0.859
Half-life (T1/2):	0.531

ADMET: Toxicity

hERG Blockers:	0.136
Human Hepatotoxicity (H-HT):	0.624
Drug-inuced Liver Injury (DILI):	0.073
AMES Toxicity:	0.014
Rat Oral Acute Toxicity:	0.822
Maximum Recommended Daily Dose:	0.952
Skin Sensitization:	0.953
Carcinogencity:	0.818
Eye Corrosion:	0.074
Eye Irritation:	0.109
Respiratory Toxicity:	0.988

Download Data

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

Natural Product: NPC204341

Natural Product ID:	NPC204341
*Common Name:**	Norselic Acid A
IUPAC Name:	(8R,9S,10R,13S,14S,17R)-17-[(2R,5R)-5-ethyl-5-hydroxy-6-methylhept-6-en-2-yl]-10-methyl-3-oxo-8,9,11,12,14,15,16,17-octahydrocyclopenta[a]phenanthrene-13-carboxylic acid
Synonyms:
Standard InCHIKey:	RZICIXRISYIONZ-QEYQUZSWSA-N
Standard InCHI:	InChI=1S/C29H40O4/c1-6-28(33,18(2)3)15-11-19(4)23-9-10-25-22-8-7-20-17-21(30)12-14-27(20,5)24(22)13-16-29(23,25)26(31)32/h7-8,12,14,17,19,22-25,33H,2,6,9-11,13,15-16H2,1,3-5H3,(H,31,32)/t19-,22-,23-,24+,25+,27+,28-,29+/m1/s1
SMILES:	CC[C@@](CC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3C=CC4=CC(=O)C=C[C@]4(C)[C@H]3CC[C@]12C(=O)O)(C(=C)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1221577
PubChem CID:	44557570
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002031] Stigmastanes and derivatives

*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
NPO33060	crella sp.	Species	Crellidae	Eukaryota	n.a.	Antarctic	n.a.	PMID[19848433]

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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
Others	10

Activity Type	# Activity
NON-MOLECULAR	1
Organism	6
Others	3

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified	""	Activity	=	35.0	%	PMID[531700]
NPT2	Others	Unspecified	""	Activity	=	18.0	%	PMID[531700]
NPT2	Others	Unspecified	""	Activity	=	9.0	%	PMID[531700]
NPT20	Organism	Candida albicans	Candida albicans	IZ	=	8.0	mm	PMID[531700]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Activity	=	2.5	uM	PMID[531700]
NPT19	Organism	Escherichia coli	Escherichia coli	IZ	=	0.0	mm	PMID[531700]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	IZ	=	8.0	mm	PMID[531700]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	IZ	=	9.0	mm	PMID[531700]
NPT1531	Organism	Enterococcus faecium	Enterococcus faecium	IZ	=	8.0	mm	PMID[531700]

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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 NPC204341 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	164
0.1-0.2	914
0.2-0.3	4433
0.3-0.4	12866
0.4-0.5	10351
0.5-0.6	7704
0.6-0.7	4592
0.7-0.8	1441
0.8-0.85	179
0.85-0.9	49
0.9-0.95	3
0.95-1	1

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Similarity Score	Similarity Level	Natural Product ID
0.9535	High Similarity	NPC262043
0.9438	High Similarity	NPC171395
0.9302	High Similarity	NPC136948
0.907	High Similarity	NPC29447
0.9059	High Similarity	NPC69279

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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 NPC204341 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	150
0.1-0.2	1180
0.2-0.3	3689
0.3-0.4	2763
0.4-0.5	838
0.5-0.6	225
0.6-0.7	168
0.7-0.8	118
0.8-0.85	14
0.85-0.9	3
0.9-0.95	2
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9101	High Similarity	NPD5284	Approved
0.9101	High Similarity	NPD5281	Approved
0.8539	High Similarity	NPD4694	Approved
0.8539	High Similarity	NPD5690	Phase 2
0.8539	High Similarity	NPD5280	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