NPASS Compound

Structure

NPC120085 OpenBabel06302215112D 27 31 0 0 1 0 0 0 0 0999 V2000 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 -4.4152 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0029 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4152 1.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.3662 1.6180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2322 1.1180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0983 1.6180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0983 2.6180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2322 3.1180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3662 2.6180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4152 2.9271 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 -3.8274 2.1180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8274 2.1180 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 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 -0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 0 0 0 2 3 1 0 0 0 0 2 23 1 0 0 0 0 3 4 1 1 0 0 0 3 20 1 0 0 0 0 4 5 1 0 0 0 0 5 18 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 8 7 1 6 0 0 0 8 16 1 0 0 0 0 8 9 1 0 0 0 0 8 18 1 0 0 0 0 9 14 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 18 19 1 6 0 0 0 20 19 1 6 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 21 24 1 0 0 0 0 22 23 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 M CHG 1 15 1 M END $$$$

Physi-Chem Properties

Molecular Weight:	368.17
Volume:	370.326
LogP:	2.807
LogD:	2.823
LogS:	-3.588
# Rotatable Bonds:	2
TPSA:	67.87
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.769
Synthetic Accessibility Score:	4.712
Fsp3:	0.524
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.769
MDCK Permeability:	2.2979093046160415e-05
Pgp-inhibitor:	0.008
Pgp-substrate:	0.042
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.481
30% Bioavailability (F30%):	0.411

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.989
Plasma Protein Binding (PPB):	65.47047424316406%
Volume Distribution (VD):	1.47
Pgp-substrate:	50.56418228149414%

ADMET: Metabolism

CYP1A2-inhibitor:	0.135
CYP1A2-substrate:	0.585
CYP2C19-inhibitor:	0.477
CYP2C19-substrate:	0.923
CYP2C9-inhibitor:	0.632
CYP2C9-substrate:	0.137
CYP2D6-inhibitor:	0.929
CYP2D6-substrate:	0.695
CYP3A4-inhibitor:	0.918
CYP3A4-substrate:	0.913

ADMET: Excretion

Clearance (CL):	4.665
Half-life (T1/2):	0.558

ADMET: Toxicity

hERG Blockers:	0.388
Human Hepatotoxicity (H-HT):	0.585
Drug-inuced Liver Injury (DILI):	0.355
AMES Toxicity:	0.697
Rat Oral Acute Toxicity:	0.749
Maximum Recommended Daily Dose:	0.927
Skin Sensitization:	0.705
Carcinogencity:	0.963
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.968

Download Data

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

Natural Product: NPC120085

Natural Product ID:	NPC120085
*Common Name:**	JMIAZDVHNCCPDM-XJKYNJMSSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JMIAZDVHNCCPDM-XJKYNJMSSA-N
Standard InCHI:	InChI=1S/C21H24N2O4/c1-12-14-10-23-8-7-21(16-5-3-4-6-17(16)22-20(21)25)18(23)9-13(14)15(11-27-12)19(24)26-2/h3-6,11-14,18H,7-10H2,1-2H3,(H,22,25)/p+1/t12-,13+,14-,18+,21-/m1/s1
SMILES:	C[C@@H]1[C@H]2CN3CC[C@@]4(c5ccccc5[NH+]=C4O)[C@@H]3C[C@@H]2C(=CO1)C(=O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	12304286
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0000013] Amino acids, peptides, and analogues [CHEMONTID:0000347] Amino acids and derivatives [CHEMONTID:0001878] Beta amino 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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO26925	Fomitopsis pinicola	Species	Fomitopsidaceae	Eukaryota	n.a.	fruit body	n.a.	PMID[15679320]
NPO26925	Fomitopsis pinicola	Species	Fomitopsidaceae	Eukaryota	fruit bodies	Tokushima, Japan	1999-Autumn	PMID[15679320]
NPO9390	Uncaria gambir	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21192716]
NPO27706	Uncaria hirsuta	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10088	Uncaria attenuata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9390	Uncaria gambir	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29352	Uncaria sinensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26925	Fomitopsis pinicola	Species	Fomitopsidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25520	Uncaria laevigata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17464	Uncaria sessilifructus	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4763	Uncaria elliptica	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9455	Uncaria orientalis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9455	Uncaria orientalis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4763	Uncaria elliptica	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10088	Uncaria attenuata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17464	Uncaria sessilifructus	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27706	Uncaria hirsuta	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9390	Uncaria gambir	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25520	Uncaria laevigata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29352	Uncaria sinensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26925	Fomitopsis pinicola	Species	Fomitopsidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9734	Vincetoxicum hirundinaria	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29352	Uncaria sinensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9390	Uncaria gambir	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29352	Uncaria sinensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26795	Pityophthorus pityographus	Species	Curculionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27706	Uncaria hirsuta	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9390	Uncaria gambir	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26925	Fomitopsis pinicola	Species	Fomitopsidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9734	Vincetoxicum hirundinaria	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10088	Uncaria attenuata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4763	Uncaria elliptica	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27246	Cercis chinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17464	Uncaria sessilifructus	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25520	Uncaria laevigata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29352	Uncaria sinensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9455	Uncaria orientalis	Species	Rubiaceae	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 NPC120085 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	190
0.1-0.2	906
0.2-0.3	2778
0.3-0.4	9791
0.4-0.5	20219
0.5-0.6	7088
0.6-0.7	1519
0.7-0.8	170
0.8-0.85	10
0.85-0.9	10
0.9-0.95	10
0.95-1	6

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 NPC120085 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	126
0.1-0.2	401
0.2-0.3	658
0.3-0.4	1116
0.4-0.5	3163
0.5-0.6	3148
0.6-0.7	527
0.7-0.8	11
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