NPASS Compound

Structure

NPC52007 OpenBabel06302216002D 48 52 0 0 1 0 0 0 0 0999 V2000 5.6164 0.0941 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9610 0.7745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2312 1.5029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4758 0.5903 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.0034 -0.2279 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.0908 -0.4724 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.7293 0.4005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0908 -1.4171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2727 -1.8895 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4545 -1.4171 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4545 -0.4724 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.5098 -0.4724 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9821 0.3458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2727 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.0282 0.9125 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.5005 1.7307 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.5731 0.9572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2230 0.5317 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.7298 -3.2150 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4793 -3.7901 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3560 -4.7267 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.3521 -3.4286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4131 1.9752 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9882 2.7247 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0515 2.8481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0915 1.0359 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7300 1.9087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3051 2.6582 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7933 2.0320 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6363 -1.8895 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8182 -1.4171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8182 -0.4724 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.8895 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8182 -1.4171 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8182 -0.4724 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6363 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6363 0.9447 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8182 1.4171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.9447 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6363 -1.8895 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 -2.4545 -1.4171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6363 -2.8342 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5785 -0.9774 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4124 0.4670 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.7740 -0.4058 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1988 -1.1553 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7106 -0.5291 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 18 1 0 0 0 0 2 3 2 0 0 0 0 3 23 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 4 45 1 0 0 0 0 5 6 1 0 0 0 0 5 44 1 6 0 0 0 6 14 1 0 0 0 0 6 7 1 1 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 10 30 1 0 0 0 0 11 13 1 0 0 0 0 11 12 1 1 0 0 0 11 14 1 0 0 0 0 12 13 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 26 1 0 0 0 0 16 17 1 0 0 0 0 16 23 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 1 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 31 33 1 0 0 0 0 33 34 1 0 0 0 0 34 35 1 0 0 0 0 34 41 1 0 0 0 0 35 40 2 0 0 0 0 35 36 1 0 0 0 0 36 37 2 0 0 0 0 37 38 1 0 0 0 0 38 39 2 0 0 0 0 39 40 1 0 0 0 0 41 42 1 0 0 0 0 41 43 1 0 0 0 0 45 46 1 0 0 0 0 46 47 2 0 0 0 0 46 48 1 0 0 0 0 M CHG 1 41 1 M END $$$$

Physi-Chem Properties

Molecular Weight:	669.35
Volume:	683.533
LogP:	3.979
LogD:	3.136
LogS:	-4.447
# Rotatable Bonds:	12
TPSA:	141.2
# H-Bond Aceptor:	11
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.183
Synthetic Accessibility Score:	6.307
Fsp3:	0.676
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:	-5.328
MDCK Permeability:	9.969326492864639e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.999
Human Intestinal Absorption (HIA):	0.03
20% Bioavailability (F20%):	0.067
30% Bioavailability (F30%):	0.666

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.007
Plasma Protein Binding (PPB):	81.73172760009766%
Volume Distribution (VD):	2.671
Pgp-substrate:	13.624999046325684%

ADMET: Metabolism

CYP1A2-inhibitor:	0.011
CYP1A2-substrate:	0.038
CYP2C19-inhibitor:	0.018
CYP2C19-substrate:	0.786
CYP2C9-inhibitor:	0.128
CYP2C9-substrate:	0.051
CYP2D6-inhibitor:	0.626
CYP2D6-substrate:	0.272
CYP3A4-inhibitor:	0.729
CYP3A4-substrate:	0.83

ADMET: Excretion

Clearance (CL):	3.884
Half-life (T1/2):	0.068

ADMET: Toxicity

hERG Blockers:	0.726
Human Hepatotoxicity (H-HT):	0.981
Drug-inuced Liver Injury (DILI):	0.942
AMES Toxicity:	0.031
Rat Oral Acute Toxicity:	0.599
Maximum Recommended Daily Dose:	0.942
Skin Sensitization:	0.151
Carcinogencity:	0.013
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.926

Download Data

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

Natural Product: NPC52007

Natural Product ID:	NPC52007
*Common Name:**	SSMQJZMZRRHBGA-YRQVDWLDSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SSMQJZMZRRHBGA-YRQVDWLDSA-N
Standard InCHI:	InChI=1S/C37H51NO10/c1-20-27(45-21(2)39)17-25-31(46-22(3)40)33-36(7,34(43)32(47-23(4)41)30(20)35(25,5)6)16-15-28(37(33)19-44-37)48-29(42)18-26(38(8)9)24-13-11-10-12-14-24/h10-14,25-28,31-34,43H,15-19H2,1-9H3/p+1/t25-,26+,27-,28-,31+,32+,33-,34-,36+,37-/m0/s1
SMILES:	CC1=C2[C@H]([C@@H]([C@]3(C)CC[C@@H]([C@@]4(CO4)[C@H]3[C@@H]([C@H](C[C@@H]1OC(=O)C)C2(C)C)OC(=O)C)OC(=O)C[C@H](c1ccccc1)[NH+](C)C)O)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	5321433
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0000676] Taxanes 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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO5589	Trichoderma koningii	Species	Hypocreaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/0038-0717(88)90050-8]
NPO5049	Garcinia multiflora	Species	Clusiaceae	Eukaryota	stems	n.a.	n.a.	PMID[12932126]
NPO16252	Microdochium bolleyi	Species	Microdochiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18510362]
NPO5589	Trichoderma koningii	Species	Hypocreaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20384316]
NPO5049	Garcinia multiflora	Species	Clusiaceae	Eukaryota	twigs	n.a.	n.a.	PMID[20681570]
NPO5049	Garcinia multiflora	Species	Clusiaceae	Eukaryota	Twigs and leaves	Taichung, Taiwan	1993-Aug	PMID[9322359]
NPO5049	Garcinia multiflora	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17476	Austrotaxus spicata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18025	Boerhavia diffusa	Species	Nyctaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5049	Garcinia multiflora	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12371	Artocarpus nobilis	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17476	Austrotaxus spicata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17476	Austrotaxus spicata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5049	Garcinia multiflora	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5049	Garcinia multiflora	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17476	Austrotaxus spicata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5589	Trichoderma koningii	Species	Hypocreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18025	Boerhavia diffusa	Species	Nyctaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12371	Artocarpus nobilis	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16252	Microdochium bolleyi	Species	Microdochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ 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

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ 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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC52007 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	187
0.1-0.2	816
0.2-0.3	2016
0.3-0.4	5999
0.4-0.5	18560
0.5-0.6	13829
0.6-0.7	1198
0.7-0.8	88
0.8-0.85	1
0.85-0.9	3
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID

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 NPC52007 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	122
0.1-0.2	433
0.2-0.3	870
0.3-0.4	2206
0.4-0.5	3446
0.5-0.6	1814
0.6-0.7	250
0.7-0.8	9
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

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