NPASS Compound

Structure

NPC125624 OpenBabel06302216172D 30 33 0 0 1 0 0 0 0 0999 V2000 2.5981 -1.5000 0.0000 C 0 0 0 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 1.7321 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 0 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 1.7321 -2.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -3.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7170 -4.4888 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3972 -5.2219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3944 -5.1472 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9577 -4.3209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6629 -3.3653 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 C 0 0 0 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 -3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 C 0 0 0 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 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8632 -3.5747 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2971 -4.4757 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 6 0 0 0 3 5 1 0 0 0 0 5 27 1 0 0 0 0 5 6 2 0 0 0 0 6 17 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 14 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 9 15 1 0 0 0 0 9 29 1 1 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 15 16 2 0 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 1 0 0 0 18 26 1 0 0 0 0 19 20 1 0 0 0 0 20 25 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 24 25 1 0 0 0 0 26 27 2 0 0 0 0 26 28 1 0 0 0 0 29 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	496.09
Volume:	445.438
LogP:	0.651
LogD:	0.233
LogS:	-1.521
# Rotatable Bonds:	7
TPSA:	251.74
# H-Bond Aceptor:	14
# H-Bond Donor:	9
# Rings:	3
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.189
Synthetic Accessibility Score:	4.149
Fsp3:	0.286
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.748
MDCK Permeability:	2.1919291611993685e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.342
Human Intestinal Absorption (HIA):	0.773
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.095
Plasma Protein Binding (PPB):	86.92615509033203%
Volume Distribution (VD):	0.599
Pgp-substrate:	13.16388988494873%

ADMET: Metabolism

CYP1A2-inhibitor:	0.345
CYP1A2-substrate:	0.016
CYP2C19-inhibitor:	0.015
CYP2C19-substrate:	0.029
CYP2C9-inhibitor:	0.227
CYP2C9-substrate:	0.048
CYP2D6-inhibitor:	0.005
CYP2D6-substrate:	0.099
CYP3A4-inhibitor:	0.053
CYP3A4-substrate:	0.005

ADMET: Excretion

Clearance (CL):	5.332
Half-life (T1/2):	0.951

ADMET: Toxicity

hERG Blockers:	0.052
Human Hepatotoxicity (H-HT):	0.174
Drug-inuced Liver Injury (DILI):	0.841
AMES Toxicity:	0.031
Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.014
Skin Sensitization:	0.693
Carcinogencity:	0.009
Eye Corrosion:	0.004
Eye Irritation:	0.812
Respiratory Toxicity:	0.02

Download Data

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

Natural Product: NPC125624

Natural Product ID:	NPC125624
*Common Name:**	HFZOLZVOTSSKSM-LPXYKDPNSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HFZOLZVOTSSKSM-LPXYKDPNSA-N
Standard InCHI:	InChI=1S/C23H25N3O4/c1-4-15(2)18-19-25-21-23(29-3,12-8-9-13-30-21)22(28)26(19)17(20(27)24-18)14-16-10-6-5-7-11-16/h5-13,15,17H,4,14H2,1-3H3,(H,24,27)/t15-,17+,23-/m1/s1
SMILES:	CC[C@@H](C)C1=C2N=C3[C@](C=CC=CO3)(C(=O)N2[C@@H](Cc2ccccc2)C(=N1)O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	51003508
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:0000060] Alpha 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
NPO10205	Aspergillus puniceus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31095389]
NPO10205	Aspergillus puniceus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21402	Vespula vulgaris	Species	Vespidae	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

Activity Type	# Activity
EC50	1
IC50	6
Others	5

Activity Type	# Activity
Individual Protein	8
Organism	4

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1794	Individual Protein	LXR-alpha	Homo sapiens	FC	=	2.7	n.a.	PMID[31095389]
NPT1794	Individual Protein	LXR-alpha	Homo sapiens	EC50	=	41000.0	nM	PMID[31095389]
NPT1210	Individual Protein	T-cell protein-tyrosine phosphatase	Homo sapiens	IC50	=	14000.0	nM	PMID[31095389]
NPT205	Individual Protein	Protein-tyrosine phosphatase 1C	Homo sapiens	IC50	=	14000.0	nM	PMID[31095389]
NPT206	Individual Protein	Protein-tyrosine phosphatase 2C	Homo sapiens	IC50	=	14000.0	nM	PMID[31095389]
NPT3914	Individual Protein	Tyrosine-protein phosphatase non-receptor type 9	Homo sapiens	IC50	=	14000.0	nM	PMID[31095389]
NPT178	Individual Protein	Protein-tyrosine phosphatase 1B	Homo sapiens	IC50	=	14000.0	nM	PMID[31095389]
NPT1078	Individual Protein	Indoleamine 2,3-dioxygenase	Homo sapiens	IC50	=	14000.0	nM	PMID[31095389]
NPT3655	Organism	Cochliobolus australiensis	Cochliobolus australiensis	GI	<	50.0	%	PMID[31095389]
NPT562	Organism	Colletotrichum gloeosporioides	Colletotrichum gloeosporioides	GI	<	50.0	%	PMID[31095389]
NPT637	Organism	Fusarium oxysporum	Fusarium oxysporum	GI	<	50.0	%	PMID[31095389]
NPT826	Organism	Magnaporthe oryzae	Magnaporthe oryzae	GI	<	50.0	%	PMID[31095389]

☑ 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 NPC125624 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	163
0.1-0.2	1010
0.2-0.3	5312
0.3-0.4	13896
0.4-0.5	19358
0.5-0.6	2380
0.6-0.7	562
0.7-0.8	14
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	1

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 NPC125624 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	114
0.1-0.2	423
0.2-0.3	769
0.3-0.4	1893
0.4-0.5	4061
0.5-0.6	1772
0.6-0.7	117
0.7-0.8	1
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