NPASS Compound

Structure

NPC475641 OpenBabel07101718202D 46 51 0 0 1 0 0 0 0 0999 V2000 -0.2788 3.3781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0850 -1.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0491 -1.0570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 2.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3578 2.2226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7810 3.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4152 6.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 5.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2812 5.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 4.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2812 4.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2989 2.3968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8867 3.2058 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 1.8171 2.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4152 1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3479 3.7058 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0491 -1.0570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5878 2.4271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 -1.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4152 4.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3479 2.7058 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5388 2.1180 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5878 0.8090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.8171 1.8090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.4152 0.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.5491 1.8090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9511 3.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.6180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 -0.1910 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.6831 0.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9511 0.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.4152 3.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 -0.1910 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.6831 1.3090 0.0000 C 0 0 2 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 3.5491 -1.9230 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 -2.6910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2812 -0.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 4.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2812 2.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0850 2.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2989 4.0148 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 -1.1910 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 3.5491 2.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 19 1 0 0 0 0 2 20 1 0 0 0 0 6 42 1 0 0 0 0 7 8 2 0 0 0 0 7 9 1 0 0 0 0 8 10 1 0 0 0 0 9 11 2 0 0 0 0 10 21 2 0 0 0 0 11 21 1 0 0 0 0 12 13 2 0 0 0 0 12 22 1 0 0 0 0 13 43 1 0 0 0 0 14 23 1 0 0 0 0 15 25 1 0 0 0 0 15 28 1 0 0 0 0 16 26 1 0 0 0 0 16 27 1 0 0 0 0 17 22 2 0 0 0 0 17 43 1 0 0 0 0 18 34 1 0 0 0 0 18 37 2 0 0 0 0 19 23 1 0 0 0 0 19 29 2 0 0 0 0 20 38 2 0 0 0 0 20 44 1 0 0 0 0 21 33 1 0 0 0 0 23 22 1 1 0 0 0 24 14 1 6 0 0 0 24 29 1 0 0 0 0 24 45 1 0 0 0 0 25 35 1 1 0 0 0 25 36 1 0 0 0 0 26 34 1 1 0 0 0 26 39 1 0 0 0 0 27 35 1 1 0 0 0 27 46 1 0 0 0 0 28 40 2 0 0 0 0 28 42 1 0 0 0 0 29 36 1 0 0 0 0 30 31 1 0 0 0 0 30 32 1 0 0 0 0 30 44 1 1 0 0 0 31 34 1 6 0 0 0 31 35 1 0 0 0 0 32 36 1 1 0 0 0 32 45 1 0 0 0 0 33 41 2 0 0 0 0 33 46 1 0 0 0 0 34 3 1 6 0 0 0 35 4 1 6 0 0 0 36 5 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	634.28
Volume:	641.411
LogP:	3.249
LogD:	2.252
LogS:	-4.751
# Rotatable Bonds:	10
TPSA:	138.57
# H-Bond Aceptor:	10
# H-Bond Donor:	1
# Rings:	6
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.196
Synthetic Accessibility Score:	5.393
Fsp3:	0.556
Lipinski Rule-of-5:	Accepted
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:	-5.258
MDCK Permeability:	5.962197610642761e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.121
20% Bioavailability (F20%):	0.965
30% Bioavailability (F30%):	0.983

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.872
Plasma Protein Binding (PPB):	76.31279754638672%
Volume Distribution (VD):	2.373
Pgp-substrate:	13.852192878723145%

ADMET: Metabolism

CYP1A2-inhibitor:	0.024
CYP1A2-substrate:	0.07
CYP2C19-inhibitor:	0.053
CYP2C19-substrate:	0.086
CYP2C9-inhibitor:	0.691
CYP2C9-substrate:	0.024
CYP2D6-inhibitor:	0.371
CYP2D6-substrate:	0.04
CYP3A4-inhibitor:	0.936
CYP3A4-substrate:	0.582

ADMET: Excretion

Clearance (CL):	8.274
Half-life (T1/2):	0.605

ADMET: Toxicity

hERG Blockers:	0.688
Human Hepatotoxicity (H-HT):	0.936
Drug-inuced Liver Injury (DILI):	0.838
AMES Toxicity:	0.012
Rat Oral Acute Toxicity:	0.856
Maximum Recommended Daily Dose:	0.972
Skin Sensitization:	0.254
Carcinogencity:	0.047
Eye Corrosion:	0.003
Eye Irritation:	0.017
Respiratory Toxicity:	0.969

Download Data

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

Natural Product: NPC475641

Natural Product ID:	NPC475641
*Common Name:**	PONWNFBYSMNLAS-GBCPFXQBSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PONWNFBYSMNLAS-GBCPFXQBSA-N
Standard InCHI:	InChI=1S/C36H42O10/c1-19-23(22-12-13-43-17-22)14-24-29(19)36(5)25(15-28(40)42-6)35(4)27(46-33(41)21-10-8-7-9-11-21)16-26(39)34(3,18-37)31(35)30(32(36)45-24)44-20(2)38/h7-13,17-18,23-27,30-32,39H,14-16H2,1-6H3/t23-,24-,25+,26-,27+,30-,31+,32-,34-,35+,36-/m1/s1
SMILES:	COC(=O)C[C@H]1[C@@]2(C)[C@@H](OC(=O)c3ccccc3)C[C@H]([C@@]([C@@H]2[C@H]([C@@H]2[C@@]1(C)C1=C(C)[C@@H](C[C@H]1O2)c1ccoc1)OC(=O)C)(C)C=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL510032
PubChem CID:	44584369
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids [CHEMONTID:0002380] Limonoids

*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
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[3701342]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[33253570]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	n.a.	ripe fruit	n.a.	PMID[16205005]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	n.a.	Brazilian	n.a.	PMID[15387656]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18932	Melia azedarach	Species	Meliaceae	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
Others	1

Activity Type	# Activity
Organism	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT140	Organism	Artemia	Artemia	Activity	=	100.0	%	PMID[556223]

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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 NPC475641 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	350
0.1-0.2	1331
0.2-0.3	2707
0.3-0.4	5090
0.4-0.5	10544
0.5-0.6	8551
0.6-0.7	7244
0.7-0.8	6247
0.8-0.85	469
0.85-0.9	133
0.9-0.95	29
0.95-1	2

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC475237
0.9688	High Similarity	NPC118086
0.9437	High Similarity	NPC62692
0.9437	High Similarity	NPC61967
0.9437	High Similarity	NPC27541

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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 NPC475641 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	302
0.1-0.2	777
0.2-0.3	1602
0.3-0.4	2572
0.4-0.5	2261
0.5-0.6	1139
0.6-0.7	386
0.7-0.8	106
0.8-0.85	5
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
0.8728	High Similarity	NPD8434	Phase 2
0.8424	Intermediate Similarity	NPD5761	Phase 2
0.8424	Intermediate Similarity	NPD5760	Phase 2
0.7921	Intermediate Similarity	NPD6765	Approved
0.7921	Intermediate Similarity	NPD6764	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