NPASS Compound

Structure

NPC475670 OpenBabel07101718302D 51 58 0 0 1 0 0 0 0 0999 V2000 -2.4271 -2.7634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2601 -2.2601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6861 -5.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8966 -1.1045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0880 0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2219 2.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3559 2.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2219 -0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3559 -0.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9540 2.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8200 1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5388 1.1180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1045 -1.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7226 -1.1810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5521 -0.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6180 -2.1756 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9511 -1.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.8200 -4.6910 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.0880 2.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8200 2.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3559 1.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2219 0.8090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4899 0.8090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7045 -2.5823 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 8.5521 -1.6910 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9511 0.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.9540 0.8090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.5388 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.9540 -5.1910 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.6861 -2.1910 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.0880 -4.6910 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.0880 -3.6910 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.8200 -1.6910 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.9540 -3.1910 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.8200 -0.6910 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4899 -0.1910 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.0880 1.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.6861 2.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6000 -3.5768 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.4181 -2.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9540 -6.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6861 -3.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2219 -5.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2219 -3.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6861 -0.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9135 -0.5933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.8200 -3.6910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9540 -0.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9540 -2.1910 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 17 1 0 0 0 0 6 7 1 0 0 0 0 6 19 2 0 0 0 0 8 9 1 0 0 0 0 8 22 1 0 0 0 0 9 36 1 0 0 0 0 10 19 1 0 0 0 0 10 20 1 0 0 0 0 11 20 1 0 0 0 0 11 27 1 0 0 0 0 12 23 1 0 0 0 0 13 24 1 0 0 0 0 14 16 1 0 0 0 0 14 47 1 0 0 0 0 15 25 1 0 0 0 0 15 46 1 0 0 0 0 16 1 1 1 0 0 0 16 24 1 0 0 0 0 17 28 1 0 0 0 0 17 38 1 6 0 0 0 18 3 1 1 0 0 0 18 29 1 0 0 0 0 18 48 1 0 0 0 0 19 37 1 0 0 0 0 20 39 1 1 0 0 0 21 7 1 6 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 22 37 1 1 0 0 0 23 36 1 1 0 0 0 24 40 1 6 0 0 0 25 30 1 0 0 0 0 25 41 1 6 0 0 0 26 12 1 1 0 0 0 26 28 1 0 0 0 0 26 51 1 0 0 0 0 27 37 1 1 0 0 0 27 49 1 0 0 0 0 28 36 1 1 0 0 0 29 31 1 0 0 0 0 29 42 1 6 0 0 0 30 33 1 0 0 0 0 30 43 1 6 0 0 0 31 32 1 0 0 0 0 31 44 1 1 0 0 0 32 34 1 0 0 0 0 32 45 1 1 0 0 0 33 35 1 0 0 0 0 33 50 1 1 0 0 0 34 48 1 0 0 0 0 34 50 1 6 0 0 0 35 46 1 0 0 0 0 35 49 1 6 0 0 0 36 4 1 1 0 0 0 37 5 1 1 0 0 0 38 13 1 1 0 0 0 38 47 1 0 0 0 0 38 51 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	724.4
Volume:	708.989
LogP:	2.078
LogD:	2.293
LogS:	-4.363
# Rotatable Bonds:	4
TPSA:	196.99
# H-Bond Aceptor:	13
# H-Bond Donor:	7
# Rings:	8
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.203
Synthetic Accessibility Score:	6.491
Fsp3:	0.947
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:	-6.039
MDCK Permeability:	7.144776463974267e-05
Pgp-inhibitor:	0.825
Pgp-substrate:	0.991
Human Intestinal Absorption (HIA):	0.749
20% Bioavailability (F20%):	0.025
30% Bioavailability (F30%):	0.976

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.052
Plasma Protein Binding (PPB):	47.60862731933594%
Volume Distribution (VD):	0.321
Pgp-substrate:	24.484394073486328%

ADMET: Metabolism

CYP1A2-inhibitor:	0.001
CYP1A2-substrate:	0.862
CYP2C19-inhibitor:	0.005
CYP2C19-substrate:	0.404
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.007
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.068
CYP3A4-inhibitor:	0.052
CYP3A4-substrate:	0.078

ADMET: Excretion

Clearance (CL):	1.014
Half-life (T1/2):	0.629

ADMET: Toxicity

hERG Blockers:	0.931
Human Hepatotoxicity (H-HT):	0.254
Drug-inuced Liver Injury (DILI):	0.043
AMES Toxicity:	0.091
Rat Oral Acute Toxicity:	0.176
Maximum Recommended Daily Dose:	0.898
Skin Sensitization:	0.9
Carcinogencity:	0.544
Eye Corrosion:	0.003
Eye Irritation:	0.012
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: NPC475670

Natural Product ID:	NPC475670
*Common Name:**	CEUOJNPNKKLCDB-VVFBCDONSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CEUOJNPNKKLCDB-VVFBCDONSA-N
Standard InCHI:	InChI=1S/C38H60O13/c1-16-14-47-38(13-24(16)40)17(2)28-26(51-38)12-23-21-7-6-19-10-20(39)11-27(37(19,5)22(21)8-9-36(23,28)4)49-35-33(30(43)25(41)15-46-35)50-34-32(45)31(44)29(42)18(3)48-34/h6,16-18,20-35,39-45H,7-15H2,1-5H3/t16-,17-,18-,20+,21+,22-,23-,24-,25-,26-,27+,28-,29-,30-,31+,32+,33+,34-,35-,36-,37-,38+/m0/s1
SMILES:	CC1COC2(CC1O)C(C3C(O2)CC4C3(CCC5C4CC=C6C5(C(CC(C6)O)OC7C(C(C(CO7)O)O)OC8C(C(C(C(O8)C)O)O)O)C)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL511017
PubChem CID:	11181702
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001013] Steroidal glycosides [CHEMONTID:0002364] Steroidal saponins

*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
NPO29813	Ornithogalum thyrsoides	Species	Hyacinthaceae	Eukaryota	bulbs	n.a.	n.a.	PMID[15497941]
NPO29813	Ornithogalum thyrsoides	Species	Hyacinthaceae	Eukaryota	bulbs	n.a.	n.a.	PMID[12398536]
NPO29813	Ornithogalum thyrsoides	Species	Hyacinthaceae	Eukaryota	n.a.	bulb	n.a.	PMID[12398536]

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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	2

Activity Type	# Activity
Cell Line	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT116	Cell Line	HL-60	Homo sapiens	IC50	=	5.2	ug.mL-1	PMID[493357]
NPT924	Cell Line	HSC-2	Homo sapiens	IC50	>	100.0	ug.mL-1	PMID[493357]

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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 NPC475670 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	307
0.1-0.2	2116
0.2-0.3	6998
0.3-0.4	13964
0.4-0.5	8600
0.5-0.6	5431
0.6-0.7	3022
0.7-0.8	1391
0.8-0.85	520
0.85-0.9	192
0.9-0.95	76
0.95-1	80

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC306131
1.0	High Similarity	NPC70204
1.0	High Similarity	NPC477027
1.0	High Similarity	NPC477026
0.99	High Similarity	NPC476539

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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 NPC475670 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	245
0.1-0.2	2279
0.2-0.3	4384
0.3-0.4	1474
0.4-0.5	406
0.5-0.6	244
0.6-0.7	90
0.7-0.8	14
0.8-0.85	9
0.85-0.9	5
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8509	High Similarity	NPD8378	Approved
0.8509	High Similarity	NPD8380	Approved
0.8509	High Similarity	NPD8296	Approved
0.8509	High Similarity	NPD8379	Approved
0.8509	High Similarity	NPD8335	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