NPASS Compound

Structure

NPC474834 OpenBabel07101719142D 34 37 0 0 1 0 0 0 0 0999 V2000 5.7036 2.7070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8376 4.2070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3735 -1.7930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7036 -0.2930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2199 2.4231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1055 -1.7930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9716 -1.2930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9716 2.7070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8376 1.2070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8376 3.2070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2395 -1.2930 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.8376 0.2070 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3689 1.4342 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9716 1.7070 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.9716 -0.2930 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.2395 -0.2930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1055 1.2070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1055 0.2070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6744 0.2313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 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 2 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7436 -0.1340 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 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 -2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 12 1 0 0 0 0 2 12 1 0 0 0 0 5 15 1 0 0 0 0 6 16 1 0 0 0 0 7 8 1 0 0 0 0 7 13 1 0 0 0 0 9 12 2 0 0 0 0 10 14 1 0 0 0 0 10 17 1 0 0 0 0 11 19 1 0 0 0 0 11 32 1 0 0 0 0 13 3 1 6 0 0 0 13 20 1 0 0 0 0 14 4 1 6 0 0 0 14 18 1 0 0 0 0 15 21 2 0 0 0 0 15 26 1 0 0 0 0 16 28 2 0 0 0 0 16 33 1 0 0 0 0 17 9 1 6 0 0 0 17 21 1 0 0 0 0 18 8 1 1 0 0 0 18 22 1 0 0 0 0 19 23 1 0 0 0 0 19 33 1 1 0 0 0 20 22 2 0 0 0 0 20 24 1 0 0 0 0 21 22 1 0 0 0 0 23 25 1 0 0 0 0 23 29 1 1 0 0 0 24 26 2 0 0 0 0 24 30 1 0 0 0 0 25 27 1 0 0 0 0 25 31 1 6 0 0 0 26 34 1 0 0 0 0 27 32 1 0 0 0 0 27 34 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	474.26
Volume:	489.672
LogP:	4.997
LogD:	3.518
LogS:	-3.572
# Rotatable Bonds:	5
TPSA:	105.45
# H-Bond Aceptor:	7
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.444
Synthetic Accessibility Score:	4.884
Fsp3:	0.667
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.08
MDCK Permeability:	2.6996283850166947e-05
Pgp-inhibitor:	0.886
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.071
20% Bioavailability (F20%):	0.823
30% Bioavailability (F30%):	0.455

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.186
Plasma Protein Binding (PPB):	94.8997573852539%
Volume Distribution (VD):	1.132
Pgp-substrate:	6.9597578048706055%

ADMET: Metabolism

CYP1A2-inhibitor:	0.034
CYP1A2-substrate:	0.137
CYP2C19-inhibitor:	0.015
CYP2C19-substrate:	0.891
CYP2C9-inhibitor:	0.093
CYP2C9-substrate:	0.725
CYP2D6-inhibitor:	0.026
CYP2D6-substrate:	0.133
CYP3A4-inhibitor:	0.212
CYP3A4-substrate:	0.492

ADMET: Excretion

Clearance (CL):	2.443
Half-life (T1/2):	0.385

ADMET: Toxicity

hERG Blockers:	0.252
Human Hepatotoxicity (H-HT):	0.926
Drug-inuced Liver Injury (DILI):	0.719
AMES Toxicity:	0.286
Rat Oral Acute Toxicity:	0.758
Maximum Recommended Daily Dose:	0.982
Skin Sensitization:	0.529
Carcinogencity:	0.423
Eye Corrosion:	0.003
Eye Irritation:	0.06
Respiratory Toxicity:	0.951

Download Data

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

Natural Product: NPC474834

Natural Product ID:	NPC474834
*Common Name:**	Pseudopterosin U
IUPAC Name:	[(3R,4S,5S,6R)-6-[[(4S,6S,6aR,9S)-1-hydroxy-3,6,9-trimethyl-4-(2-methylprop-1-enyl)-5,6,6a,7,8,9-hexahydro-4H-phenalen-2-yl]oxy]-4,5-dihydroxyoxan-3-yl] acetate
Synonyms:	Pseudopterosin U
Standard InCHIKey:	GKCBYTVPJRUVKI-JWJDLXRRSA-N
Standard InCHI:	InChI=1S/C27H38O7/c1-12(2)9-17-10-14(4)18-8-7-13(3)20-22(18)21(17)15(5)26(24(20)30)34-27-25(31)23(29)19(11-32-27)33-16(6)28/h9,13-14,17-19,23,25,27,29-31H,7-8,10-11H2,1-6H3/t13-,14-,17+,18+,19+,23+,25-,27+/m0/s1
SMILES:	CC(=O)O[C@@H]1CO[C@@H]([C@H]([C@@H]1O)O)Oc1c(C)c2[C@H](C=C(C)C)C[C@@H]([C@@H]3c2c(c1O)[C@@H](C)CC3)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL484438
PubChem CID:	11454321
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0003398] Amphilectane, neoamphilectane, cycloamphilectane, and adociane 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
NPO31261	Pseudopterogorgia elisabethae	Species	Gorgoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[21978379]
NPO31261	Pseudopterogorgia elisabethae	Species	Gorgoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[17715964]
NPO31261	Pseudopterogorgia elisabethae	Species	Gorgoniidae	Eukaryota	n.a.	Colombian	n.a.	PMID[15497938]
NPO31261	Pseudopterogorgia elisabethae	Species	Gorgoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[12828474]
NPO31261	Pseudopterogorgia elisabethae	Species	Gorgoniidae	Eukaryota	n.a.	West Indian sea	n.a.	PMID[11170678]
NPO31261	Pseudopterogorgia elisabethae	Species	Gorgoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[10822593]
NPO31261	Pseudopterogorgia elisabethae	Species	Gorgoniidae	Eukaryota	n.a.	West Indian sea	n.a.	PMID[10425124]

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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
GI50	1
IC50	3
Others	5

Activity Type	# Activity
Cell Line	3
NON-MOLECULAR	4
Organism	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT83	Cell Line	MCF7	Homo sapiens	Activity	=	0.0	%	PMID[464756]
NPT397	Cell Line	NCI-H460	Homo sapiens	Activity	=	0.0	%	PMID[464756]
NPT395	Cell Line	SF-268	Homo sapiens	Activity	=	0.0	%	PMID[464756]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	GI50	=	20000.0	nM	PMID[464756]
NPT88	Organism	Mycobacterium tuberculosis	Mycobacterium tuberculosis	Inhibition	=	43.0	%	PMID[464756]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	19.0	ug.mL-1	PMID[464756]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	14700.0	nM	PMID[464756]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	10000.0	nM	PMID[464756]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Activity	=	0.7	uM	PMID[464756]

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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 NPC474834 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	324
0.1-0.2	1456
0.2-0.3	3474
0.3-0.4	7710
0.4-0.5	10228
0.5-0.6	6286
0.6-0.7	8913
0.7-0.8	4000
0.8-0.85	244
0.85-0.9	43
0.9-0.95	4
0.95-1	15

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC117788
1.0	High Similarity	NPC474856
1.0	High Similarity	NPC290902
1.0	High Similarity	NPC291326
0.9929	High Similarity	NPC475940

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 NPC474834 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	269
0.1-0.2	926
0.2-0.3	1993
0.3-0.4	2741
0.4-0.5	1723
0.5-0.6	957
0.6-0.7	463
0.7-0.8	76
0.8-0.85	1
0.85-0.9	0
0.9-0.95	1
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.95	High Similarity	NPD6674	Discontinued
0.8333	Intermediate Similarity	NPD7228	Approved
0.8125	Intermediate Similarity	NPD6234	Discontinued
0.8038	Intermediate Similarity	NPD37	Approved
0.8	Intermediate Similarity	NPD4967	Phase 2

Showing 1 to 5 of 200 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