NPASS Compound

Structure

NPC123796 OpenBabel07101719522D 75 83 0 0 1 0 0 0 0 0999 V2000 -13.6914 -0.9881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9169 2.8319 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9288 2.8319 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2055 -3.8200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5671 -0.4940 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8557 1.4821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.9881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8557 -1.4821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7114 -0.9881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7114 1.9762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2786 0.4940 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4229 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8557 1.4821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5671 -2.4702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5671 -1.4821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8557 -2.4702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8557 0.4940 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8457 -2.9643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.2686 2.9643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7014 1.4821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2174 -3.8200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5671 -0.4940 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.8357 -1.4821 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 -0.9881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8557 -1.4821 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.9900 -2.4702 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -10.2686 1.9762 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.7014 0.4940 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5671 1.4821 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7114 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7114 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2786 1.4821 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -12.8357 -2.4702 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1343 -2.9643 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -11.1243 1.4821 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.8457 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -11.9800 -2.9643 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2786 -2.4702 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -11.1243 0.4940 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -11.1243 -2.4702 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2786 -1.4821 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.9900 0.4940 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -10.2686 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -11.1243 -1.4821 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1343 -0.9881 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.9900 1.4821 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -9.4129 0.4940 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4229 1.9762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7114 -2.9643 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5671 0.4940 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8557 0.4940 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7114 -0.9881 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.7014 -2.4702 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.1243 3.4583 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7114 -4.6757 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4229 -0.9881 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5671 0.4940 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -13.6914 -2.9643 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1343 -3.9524 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.9800 1.9762 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8457 -0.9881 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.9800 -3.9524 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4229 -2.9643 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.9800 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.2686 -2.9643 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4229 -0.9881 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8457 1.9762 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.9800 -0.9881 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9900 -1.4821 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.4129 1.4821 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.5572 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1343 1.9762 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1343 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.2686 -0.9881 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 48 1 0 0 0 0 3 48 1 0 0 0 0 6 51 1 0 0 0 0 8 9 1 0 0 0 0 8 24 2 0 0 0 0 9 30 1 0 0 0 0 10 13 1 0 0 0 0 10 29 1 0 0 0 0 11 12 1 0 0 0 0 11 32 1 0 0 0 0 12 50 1 0 0 0 0 13 51 1 0 0 0 0 14 15 1 0 0 0 0 14 49 1 0 0 0 0 15 53 1 0 0 0 0 16 25 1 0 0 0 0 16 49 1 0 0 0 0 17 31 1 0 0 0 0 17 52 1 0 0 0 0 18 54 1 0 0 0 0 19 55 1 0 0 0 0 20 28 1 0 0 0 0 20 68 1 0 0 0 0 21 49 1 0 0 0 0 21 56 1 0 0 0 0 22 57 1 0 0 0 0 23 1 1 6 0 0 0 23 33 1 0 0 0 0 23 69 1 0 0 0 0 24 25 1 0 0 0 0 24 52 1 0 0 0 0 25 53 1 1 0 0 0 26 18 1 1 0 0 0 26 34 1 0 0 0 0 26 70 1 0 0 0 0 27 19 1 1 0 0 0 27 35 1 0 0 0 0 27 71 1 0 0 0 0 28 36 1 0 0 0 0 28 72 1 1 0 0 0 29 48 1 0 0 0 0 29 50 1 6 0 0 0 30 50 1 6 0 0 0 30 51 1 0 0 0 0 31 53 1 1 0 0 0 31 58 1 0 0 0 0 32 48 1 0 0 0 0 32 73 1 6 0 0 0 33 37 1 0 0 0 0 33 59 1 1 0 0 0 34 38 1 0 0 0 0 34 60 1 6 0 0 0 35 39 1 0 0 0 0 35 61 1 6 0 0 0 36 42 1 0 0 0 0 36 62 1 1 0 0 0 37 40 1 0 0 0 0 37 63 1 6 0 0 0 38 41 1 0 0 0 0 38 64 1 1 0 0 0 39 43 1 0 0 0 0 39 65 1 1 0 0 0 40 44 1 0 0 0 0 40 66 1 6 0 0 0 41 45 1 0 0 0 0 41 67 1 6 0 0 0 42 46 1 0 0 0 0 42 74 1 6 0 0 0 43 47 1 0 0 0 0 43 75 1 6 0 0 0 44 69 1 0 0 0 0 44 75 1 1 0 0 0 45 70 1 0 0 0 0 45 74 1 1 0 0 0 46 68 1 0 0 0 0 46 73 1 1 0 0 0 47 71 1 0 0 0 0 47 72 1 1 0 0 0 49 4 1 1 0 0 0 50 5 1 6 0 0 0 51 52 1 1 0 0 0 52 7 1 1 0 0 0 53 22 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	1076.58
Volume:	1038.984
LogP:	1.335
LogD:	1.64
LogS:	-3.409
# Rotatable Bonds:	12
TPSA:	357.06
# H-Bond Aceptor:	22
# H-Bond Donor:	14
# Rings:	9
# Heavy Atoms:	22

MedChem Properties

QED Drug-Likeness Score:	0.075
Synthetic Accessibility Score:	6.921
Fsp3:	0.962
Lipinski Rule-of-5:	Rejected
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:	-6.31
MDCK Permeability:	8.426815475104377e-05
Pgp-inhibitor:	0.038
Pgp-substrate:	0.558
Human Intestinal Absorption (HIA):	0.997
20% Bioavailability (F20%):	0.129
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.149
Plasma Protein Binding (PPB):	50.56520080566406%
Volume Distribution (VD):	0.042
Pgp-substrate:	16.996641159057617%

ADMET: Metabolism

CYP1A2-inhibitor:	0.0
CYP1A2-substrate:	0.365
CYP2C19-inhibitor:	0.0
CYP2C19-substrate:	0.21
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.002
CYP2D6-inhibitor:	0.0
CYP2D6-substrate:	0.021
CYP3A4-inhibitor:	0.098
CYP3A4-substrate:	0.008

ADMET: Excretion

Clearance (CL):	0.307
Half-life (T1/2):	0.783

ADMET: Toxicity

hERG Blockers:	0.117
Human Hepatotoxicity (H-HT):	0.194
Drug-inuced Liver Injury (DILI):	0.005
AMES Toxicity:	0.067
Rat Oral Acute Toxicity:	0.079
Maximum Recommended Daily Dose:	0.882
Skin Sensitization:	0.247
Carcinogencity:	0.022
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.974

Download Data

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

Natural Product: NPC123796

Natural Product ID:	NPC123796
*Common Name:**	Ardisiamamillosede C
IUPAC Name:	(2S,3R,4R,5R,6S)-2-[(2S,3R,4S,5S,6R)-2-[(3S,4S,5R,6S)-6-[[(3S,4aR,6aR,6bS,8R,8aS,11S,12aS,14aR,14bR)-8-hydroxy-8a,11-bis(hydroxymethyl)-4,4,6a,6b,11,14b-hexamethyl-1,2,3,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydropicen-3-yl]oxy]-4-hydroxy-5-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-3-yl]oxy-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl]oxy-6-methyloxane-3,4,5-triol
Synonyms:	Ardisiamamillosede C
Standard InCHIKey:	FUEJSDQPLRTIHO-BVWKTBKYSA-N
Standard InCHI:	InChI=1S/C53H88O22/c1-23-33(59)37(63)40(66)44(69-23)75-43-39(65)35(61)27(19-55)71-47(43)72-28-20-68-46(42(36(28)62)74-45-41(67)38(64)34(60)26(18-54)70-45)73-32-11-12-50(5)29(48(32,2)3)10-13-51(6)30(50)9-8-24-25-16-49(4,21-56)14-15-53(25,22-57)31(58)17-52(24,51)7/h8,23,25-47,54-67H,9-22H2,1-7H3/t23-,25-,26+,27+,28-,29-,30+,31+,32-,33-,34+,35+,36-,37+,38-,39-,40+,41+,42+,43+,44-,45-,46-,47-,49-,50-,51+,52+,53+/m0/s1
SMILES:	C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@H]([C@@H]([C@@H](CO)O[C@H]1O[C@H]1CO[C@H]([C@@H]([C@H]1O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O[C@H]1CC[C@@]2(C)[C@@H](CC[C@]3(C)[C@@H]2CC=C2[C@@H]4C[C@](C)(CC[C@]4(CO)[C@@H](C[C@@]32C)O)CO)C1(C)C)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL426381
PubChem CID:	44419578
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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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Search:

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22940450]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[17397219]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	whole plants	Sendai, Miyagi Prefecture, Japan	2000-Sep	PMID[17243725]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[17243725]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]

Showing 1 to 9 of 9 entries

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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	6

Activity Type	# Activity
Cell Line	4
Others	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT181	Cell Line	Bel-7402	Homo sapiens	IC50	>	100000000.0	nM	PMID[546295]
NPT65	Cell Line	HepG2	Homo sapiens	IC50	>	100000000.0	nM	PMID[546295]
NPT27	Others	Unspecified	""	IC50	>	100000000.0	nM	PMID[546295]
NPT116	Cell Line	HL-60	Homo sapiens	IC50	>	100000.0	nM	PMID[546294]
NPT81	Cell Line	A549	Homo sapiens	IC50	>	100000.0	nM	PMID[546294]
NPT27	Others	Unspecified	""	IC50	>	100000.0	nM	PMID[546294]

Showing 1 to 6 of 6 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 NPC123796 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	282
0.1-0.2	2190
0.2-0.3	6197
0.3-0.4	14036
0.4-0.5	9271
0.5-0.6	5469
0.6-0.7	2741
0.7-0.8	1505
0.8-0.85	444
0.85-0.9	358
0.9-0.95	179
0.95-1	25

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Similarity Score	Similarity Level	Natural Product ID
0.9896	High Similarity	NPC148603
0.9895	High Similarity	NPC30289
0.9895	High Similarity	NPC76497
0.9895	High Similarity	NPC256133
0.9895	High Similarity	NPC213674

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 NPC123796 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	241
0.1-0.2	2425
0.2-0.3	4003
0.3-0.4	1696
0.4-0.5	434
0.5-0.6	283
0.6-0.7	43
0.7-0.8	16
0.8-0.85	9
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
0.8087	Intermediate Similarity	NPD8328	Phase 3
0.7982	Intermediate Similarity	NPD8377	Approved
0.7982	Intermediate Similarity	NPD8294	Approved
0.7913	Intermediate Similarity	NPD8296	Approved
0.7913	Intermediate Similarity	NPD8379	Approved

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