NPASS Compound

Structure

NPC470115 OpenBabel07101718182D 52 59 0 0 1 0 0 0 0 0999 V2000 0.5969 -4.6544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1350 -2.8773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3523 -2.6381 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1805 2.0492 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5378 0.2401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0560 -1.7357 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7259 -0.1212 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6319 -1.2013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2509 -4.0101 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1106 0.0482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7218 2.0865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7997 -1.1963 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1731 0.1717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6648 -1.1360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0635 0.6800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0199 -3.1216 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 4.1672 -2.2152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6867 -0.2760 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.2473 1.3337 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.0970 -0.9445 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4347 -0.8039 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.2409 0.6963 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.1565 1.8193 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.6507 1.1390 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.3784 -0.3933 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0606 0.2210 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.6507 0.2210 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.8557 1.5981 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6739 -2.4773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2136 0.3702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0457 -1.0899 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0606 1.1390 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6937 0.6013 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.8557 -0.2380 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.5239 -0.0627 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8976 0.7727 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.1739 0.9014 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.9409 -2.7094 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8557 2.5161 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5589 -2.7215 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4973 1.2433 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9814 -2.0057 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3763 2.5453 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7927 -1.1879 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8279 -0.3120 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8710 -0.6877 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5239 1.4227 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7518 -1.2320 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2084 -1.2981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2282 1.1621 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4430 -1.5887 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 9 1 0 0 0 0 2 16 1 0 0 0 0 3 17 1 0 0 0 0 5 33 1 0 0 0 0 6 44 1 0 0 0 0 7 45 1 0 0 0 0 8 46 1 0 0 0 0 9 16 1 0 0 0 0 10 18 1 0 0 0 0 10 22 1 0 0 0 0 11 19 1 0 0 0 0 11 23 1 0 0 0 0 12 20 1 0 0 0 0 12 21 1 0 0 0 0 13 18 1 0 0 0 0 13 36 1 0 0 0 0 14 48 1 0 0 0 0 15 35 1 0 0 0 0 15 47 1 0 0 0 0 16 29 1 0 0 0 0 17 38 2 0 0 0 0 17 49 1 0 0 0 0 18 44 1 6 0 0 0 19 33 1 0 0 0 0 19 36 1 0 0 0 0 20 34 1 6 0 0 0 20 51 1 0 0 0 0 21 35 1 6 0 0 0 21 49 1 0 0 0 0 22 36 1 6 0 0 0 22 50 1 0 0 0 0 23 37 1 0 0 0 0 23 50 1 0 0 0 0 24 27 1 0 0 0 0 24 28 1 0 0 0 0 24 47 1 6 0 0 0 25 26 1 0 0 0 0 25 30 1 6 0 0 0 25 48 1 0 0 0 0 26 32 1 1 0 0 0 26 34 1 0 0 0 0 27 34 1 1 0 0 0 27 35 1 0 0 0 0 28 32 1 6 0 0 0 28 39 1 0 0 0 0 29 40 2 0 0 0 0 29 51 1 0 0 0 0 30 41 2 0 0 0 0 30 45 1 0 0 0 0 31 42 2 0 0 0 0 31 46 1 0 0 0 0 32 4 1 1 0 0 0 32 37 1 0 0 0 0 33 37 1 6 0 0 0 33 52 1 0 0 0 0 34 14 1 1 0 0 0 35 31 1 1 0 0 0 36 43 1 1 0 0 0 37 52 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	736.33
Volume:	701.364
LogP:	2.281
LogD:	1.443
LogS:	-4.888
# Rotatable Bonds:	12
TPSA:	195.11
# H-Bond Aceptor:	15
# H-Bond Donor:	2
# Rings:	8
# Heavy Atoms:	15

MedChem Properties

QED Drug-Likeness Score:	0.202
Synthetic Accessibility Score:	7.531
Fsp3:	0.892
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.329
MDCK Permeability:	0.00014731961709912866
Pgp-inhibitor:	0.981
Pgp-substrate:	0.997
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.014
30% Bioavailability (F30%):	0.29

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.077
Plasma Protein Binding (PPB):	31.692800521850586%
Volume Distribution (VD):	1.1
Pgp-substrate:	49.633087158203125%

ADMET: Metabolism

CYP1A2-inhibitor:	0.001
CYP1A2-substrate:	0.991
CYP2C19-inhibitor:	0.007
CYP2C19-substrate:	0.652
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.001
CYP2D6-inhibitor:	0.008
CYP2D6-substrate:	0.071
CYP3A4-inhibitor:	0.548
CYP3A4-substrate:	0.666

ADMET: Excretion

Clearance (CL):	4.989
Half-life (T1/2):	0.124

ADMET: Toxicity

hERG Blockers:	0.508
Human Hepatotoxicity (H-HT):	0.592
Drug-inuced Liver Injury (DILI):	0.398
AMES Toxicity:	0.204
Rat Oral Acute Toxicity:	0.254
Maximum Recommended Daily Dose:	0.737
Skin Sensitization:	0.178
Carcinogencity:	0.236
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: NPC470115

Natural Product ID:	NPC470115
*Common Name:**	Vepaol
IUPAC Name:	n.a.
Synonyms:	Vepaol
Standard InCHIKey:	ZMBSZFLUIUMZOK-WOPACFSYSA-N
Standard InCHI:	InChI=1S/C37H52O15/c1-9-16(2)29(40)51-20-12-21(49-17(3)38)35(31(42)46-8)15-47-24-27(35)34(20)14-48-25(30(41)45-7)26(34)32(4,28(24)39)37-23-11-19(33(37,5)52-37)36(43)13-18(44-6)10-22(36)50-23/h16,18-28,39,43H,9-15H2,1-8H3/t16?,18-,19?,20-,21+,22+,23?,24+,25-,26-,27+,28+,32-,33-,34+,35-,36-,37-/m0/s1
SMILES:	CCC(C)C(=O)OC1CC(C2(COC3C2C14COC(C4C(C3O)(C)C56C7CC(C5(O6)C)C8(CC(CC8O7)OC)O)C(=O)OC)C(=O)OC)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1774408
PubChem CID:	54583360
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0002966] Tetracarboxylic acids 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

Show entries

Search:

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	bark	n.a.	PMID[9134742]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	fruit	n.a.	PMID[9134742]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	leaf	n.a.	PMID[9134742]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[28493718]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26339153]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2614419]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2607354]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[21381696]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	seed	n.a.	PMID[21381696]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	fruits	n.a.	n.a.	PMID[20669933]

Showing 1 to 10 of 15 entries

Previous1 2Next

☑ 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

Show entries

Search:

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

Showing 0 to 0 of 0 entries

PreviousNext

☑ 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	5

Activity Type	# Activity
Cell Line	3
NON-MOLECULAR	2

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT116	Cell Line	HL-60	Homo sapiens	IC50	>	20000.0	nM	PMID[535855]
NPT81	Cell Line	A549	Homo sapiens	IC50	>	20000.0	nM	PMID[535855]
NPT134	Cell Line	SK-BR-3	Homo sapiens	IC50	>	20000.0	nM	PMID[535855]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	20000.0	nM	PMID[535855]

Showing 1 to 4 of 4 entries

Previous1Next

☑ 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 NPC470115 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	640
0.1-0.2	4462
0.2-0.3	10132
0.3-0.4	13127
0.4-0.5	6430
0.5-0.6	5251
0.6-0.7	2272
0.7-0.8	360
0.8-0.85	16
0.85-0.9	5
0.9-0.95	0
0.95-1	2

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC470116
0.8673	High Similarity	NPC475490
0.8491	Intermediate Similarity	NPC253995
0.8387	Intermediate Similarity	NPC219058
0.8387	Intermediate Similarity	NPC256618

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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 NPC470115 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	680
0.1-0.2	4170
0.2-0.3	2916
0.3-0.4	819
0.4-0.5	317
0.5-0.6	181
0.6-0.7	62
0.7-0.8	4
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Show entries

Search:

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8679	High Similarity	NPD1700	Approved
0.7632	Intermediate Similarity	NPD4057	Clinical (unspecified phase)
0.7632	Intermediate Similarity	NPD4056	Clinical (unspecified phase)
0.7328	Intermediate Similarity	NPD8170	Clinical (unspecified phase)
0.7288	Intermediate Similarity	NPD5345	Clinical (unspecified phase)

Showing 1 to 5 of 181 entries

Previous1 2 3 4 5…37Next

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