NPASS Compound

Structure

CID239824 OpenBabel06191716042D 45 51 0 0 1 0 0 0 0 0999 V2000 4.3593 0.6050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2888 -3.2900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1282 -1.9372 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3593 -5.3950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3283 1.6373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1314 0.9705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9888 0.4978 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6881 -3.9030 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2223 1.0483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2824 0.5583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2714 -3.0128 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2254 -1.8950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8971 -1.2248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2254 -0.8950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8991 -1.9338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1576 -0.2705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4427 -2.6084 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5837 -3.5586 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4633 -0.3841 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3593 -3.3950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6273 -2.3950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6373 0.2112 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0088 -3.1692 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3593 -2.3950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2821 -0.8720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5946 0.3861 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4933 -1.8950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4933 -0.8950 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6711 -1.9372 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.1313 0.0167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7079 -2.9286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4933 -3.8950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2705 -3.7345 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6273 -3.3950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6691 -1.2282 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6182 -0.0704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4370 -0.5583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3593 -0.3950 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.2861 -2.2900 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.4793 0.9542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1318 -2.0229 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4933 -4.8950 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0197 0.6998 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 1.9772 -3.6780 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 38 1 0 0 0 0 2 39 1 0 0 0 0 3 41 1 0 0 0 0 4 42 1 0 0 0 0 5 43 1 0 0 0 0 6 9 1 0 0 0 0 6 22 2 0 0 0 0 7 10 2 0 0 0 0 7 22 1 0 0 0 0 8 11 2 0 0 0 0 8 23 1 0 0 0 0 9 26 2 0 0 0 0 10 26 1 0 0 0 0 11 31 1 0 0 0 0 12 14 1 0 0 0 0 12 24 1 0 0 0 0 13 15 1 0 0 0 0 13 25 1 0 0 0 0 14 38 1 0 0 0 0 15 39 1 0 0 0 0 16 22 1 0 0 0 0 17 23 1 0 0 0 0 18 23 2 0 0 0 0 18 33 1 0 0 0 0 19 25 2 0 0 0 0 19 30 1 0 0 0 0 20 24 2 0 0 0 0 20 32 1 0 0 0 0 21 27 2 0 0 0 0 21 34 1 0 0 0 0 24 27 1 0 0 0 0 25 35 1 0 0 0 0 26 44 1 0 0 0 0 27 28 1 0 0 0 0 28 16 1 1 0 0 0 28 38 1 0 0 0 0 29 17 1 6 0 0 0 29 35 1 0 0 0 0 29 39 1 0 0 0 0 30 36 2 0 0 0 0 30 40 1 0 0 0 0 31 33 2 0 0 0 0 31 41 1 0 0 0 0 32 34 2 0 0 0 0 32 42 1 0 0 0 0 33 45 1 0 0 0 0 34 45 1 0 0 0 0 35 37 2 0 0 0 0 36 37 1 0 0 0 0 36 43 1 0 0 0 0 37 44 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	608.29
Volume:	631.71
LogP:	6.159
LogD:	4.049
LogS:	-5.939
# Rotatable Bonds:	3
TPSA:	72.86
# H-Bond Aceptor:	8
# H-Bond Donor:	1
# Rings:	8
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.271
Synthetic Accessibility Score:	5.783
Fsp3:	0.351
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.782
MDCK Permeability:	2.5461878976784647e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.87
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.411
30% Bioavailability (F30%):	0.964

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.139
Plasma Protein Binding (PPB):	74.5873794555664%
Volume Distribution (VD):	1.05
Pgp-substrate:	16.5502986907959%

ADMET: Metabolism

CYP1A2-inhibitor:	0.077
CYP1A2-substrate:	0.968
CYP2C19-inhibitor:	0.096
CYP2C19-substrate:	0.968
CYP2C9-inhibitor:	0.051
CYP2C9-substrate:	0.62
CYP2D6-inhibitor:	0.02
CYP2D6-substrate:	0.954
CYP3A4-inhibitor:	0.102
CYP3A4-substrate:	0.953

ADMET: Excretion

Clearance (CL):	10.134
Half-life (T1/2):	0.285

ADMET: Toxicity

hERG Blockers:	0.973
Human Hepatotoxicity (H-HT):	0.034
Drug-inuced Liver Injury (DILI):	0.562
AMES Toxicity:	0.121
Rat Oral Acute Toxicity:	0.414
Maximum Recommended Daily Dose:	0.994
Skin Sensitization:	0.809
Carcinogencity:	0.042
Eye Corrosion:	0.003
Eye Irritation:	0.005
Respiratory Toxicity:	0.396

Download Data

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

Natural Product: NPC239824

Natural Product ID:	NPC239824
*Common Name:**	Racemosidine C
IUPAC Name:	n.a.
Synonyms:	Racemosidine C
Standard InCHIKey:	DQFIZQYILFTDPW-WDYNHAJCSA-N
Standard InCHI:	InChI=1S/C37H40N2O6/c1-38-14-12-24-20-32(42-4)34-21-27(24)28(38)16-22-6-9-26(10-7-22)44-37-35-25(19-30(40)36(37)43-5)13-15-39(2)29(35)17-23-8-11-31(41-3)33(18-23)45-34/h6-11,18-21,28-29,40H,12-17H2,1-5H3/t28-,29+/m1/s1
SMILES:	COc1ccc2cc1Oc1cc3c(cc1OC)CCN([C@@H]3Cc1ccc(Oc3c4[C@H](C2)N(C)CCc4cc(c3OC)O)cc1)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1172570
PubChem CID:	46872239
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000254] Ethers [CHEMONTID:0002463] Diarylethers

*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
NPO18410	Cyclea racemosa	Species	Menispermaceae	Eukaryota	roots	n.a.	n.a.	PMID[20593839]
NPO18410	Cyclea racemosa	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18410	Cyclea racemosa	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18410	Cyclea racemosa	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18410	Cyclea racemosa	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]

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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

Activity Type	# Activity
Cell Line	3

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT180	Cell Line	HCT-8	Homo sapiens	IC50	=	6040.0	nM	PMID[475337]
NPT181	Cell Line	Bel-7402	Homo sapiens	IC50	=	7530.0	nM	PMID[475337]
NPT179	Cell Line	A2780	Homo sapiens	IC50	>	10000.0	nM	PMID[475337]

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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 NPC239824 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	365
0.1-0.2	1776
0.2-0.3	8970
0.3-0.4	9442
0.4-0.5	5495
0.5-0.6	8583
0.6-0.7	6506
0.7-0.8	1271
0.8-0.85	138
0.85-0.9	45
0.9-0.95	42
0.95-1	64

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC251735
1.0	High Similarity	NPC104196
1.0	High Similarity	NPC229373
1.0	High Similarity	NPC15414
1.0	High Similarity	NPC223690

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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 NPC239824 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	208
0.1-0.2	792
0.2-0.3	1192
0.3-0.4	2208
0.4-0.5	2416
0.5-0.6	1548
0.6-0.7	643
0.7-0.8	133
0.8-0.85	3
0.85-0.9	1
0.9-0.95	3
0.95-1	3

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD8054	Approved
1.0	High Similarity	NPD8053	Approved
0.9573	High Similarity	NPD8251	Approved
0.9573	High Similarity	NPD8252	Approved
0.9573	High Similarity	NPD8099	Discontinued

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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