NPASS Compound

Structure

NPC129277 OpenBabel06302216212D 35 39 0 0 1 0 0 0 0 0999 V2000 -3.5056 -4.2071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0181 -3.3627 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8624 -2.8752 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8624 -1.9002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0181 -1.4127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1737 -1.9002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1737 -2.8752 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3293 -1.4127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3293 -0.4377 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1737 0.0498 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0181 -0.4377 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7426 0.2147 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.3461 1.1054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8336 1.9498 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3764 1.0035 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5219 1.6061 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2027 0.9537 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1300 1.2550 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3327 2.2087 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8546 0.6026 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.8242 0.7045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2208 -0.1862 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4962 -0.8386 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6518 -0.3511 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7246 -0.6524 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5219 -1.6061 0.0000 O 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 1.0788 -1.1399 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4753 -2.0306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1737 1.9572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4750 2.8845 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1274 2.1599 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2464 2.2585 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0437 3.2122 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5306 -4.2071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 7 1 0 0 0 0 2 3 1 0 0 0 0 2 35 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 5 11 1 0 0 0 0 5 6 2 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 10 15 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 13 15 1 0 0 0 0 15 16 1 6 0 0 0 15 30 1 0 0 0 0 17 16 1 1 0 0 0 17 18 1 0 0 0 0 17 27 1 0 0 0 0 18 19 2 0 0 0 0 18 20 1 0 0 0 0 20 24 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 24 28 1 1 0 0 0 25 26 2 0 0 0 0 25 27 1 0 0 0 0 28 29 1 0 0 0 0 30 31 1 0 0 0 0 30 32 1 0 0 0 0 30 33 1 0 0 0 0 33 34 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	479.24
Volume:	488.616
LogP:	3.911
LogD:	3.319
LogS:	-4.804
# Rotatable Bonds:	5
TPSA:	97.3
# H-Bond Aceptor:	8
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.646
Synthetic Accessibility Score:	5.185
Fsp3:	0.556
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.784
MDCK Permeability:	2.5967357942136005e-05
Pgp-inhibitor:	0.859
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.044
20% Bioavailability (F20%):	0.484
30% Bioavailability (F30%):	0.619

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.573
Plasma Protein Binding (PPB):	78.17273712158203%
Volume Distribution (VD):	1.414
Pgp-substrate:	18.315649032592773%

ADMET: Metabolism

CYP1A2-inhibitor:	0.037
CYP1A2-substrate:	0.822
CYP2C19-inhibitor:	0.223
CYP2C19-substrate:	0.895
CYP2C9-inhibitor:	0.434
CYP2C9-substrate:	0.218
CYP2D6-inhibitor:	0.057
CYP2D6-substrate:	0.111
CYP3A4-inhibitor:	0.942
CYP3A4-substrate:	0.944

ADMET: Excretion

Clearance (CL):	3.76
Half-life (T1/2):	0.147

ADMET: Toxicity

hERG Blockers:	0.015
Human Hepatotoxicity (H-HT):	0.496
Drug-inuced Liver Injury (DILI):	0.672
AMES Toxicity:	0.268
Rat Oral Acute Toxicity:	0.911
Maximum Recommended Daily Dose:	0.892
Skin Sensitization:	0.092
Carcinogencity:	0.961
Eye Corrosion:	0.003
Eye Irritation:	0.006
Respiratory Toxicity:	0.425

Download Data

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

Natural Product: NPC129277

Natural Product ID:	NPC129277
*Common Name:**	OCKJJINPDXBXCN-OALGXETFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	OCKJJINPDXBXCN-OALGXETFSA-N
Standard InCHI:	InChI=1S/C27H33N3O5/c1-7-24(2,3)26(15-18-21(31)30-14-8-12-27(30,34-6)23(33)28-18)17-9-10-19-16(20(17)29-22(26)32)11-13-25(4,5)35-19/h7,9-11,13,18H,1,8,12,14-15H2,2-6H3,(H,28,33)(H,29,32)/t18-,26-,27-/m0/s1
SMILES:	C=CC(C)(C)[C@@]1(C[C@H]2C(=O)N3CCC[C@@]3(C(=N2)O)OC)c2ccc3c(C=CC(C)(C)O3)c2N=C1O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	71665368
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000123] Benzopyrans [CHEMONTID:0003410] 1-benzopyrans [CHEMONTID:0003522] 2,2-dimethyl-1-benzopyrans

*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
NPO31572	Aspergillus sp.	Species	Aspergillaceae	Eukaryota	rhizosphere	Sonoran desert	n.a.	PMID[15620238]
NPO31572	Aspergillus sp.	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17542490]
NPO31572	Aspergillus sp.	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17564467]
NPO31572	Aspergillus sp.	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19053517]
NPO31572	Aspergillus sp.	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21366228]
NPO31572	Aspergillus sp.	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21718031]
NPO31572	Aspergillus sp.	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21854017]
NPO31572	Aspergillus sp.	Species	Aspergillaceae	Eukaryota	healthy leaf of Ginkgo biloba	campus of Nanjing University, Nanjing, China	2008-OCT	PMID[22196792]
NPO31572	Aspergillus sp.	Species	Aspergillaceae	Eukaryota	isolated from the sponge Xestospongia testudinaria	n.a.	n.a.	PMID[22225637]
NPO31572	Aspergillus sp.	Species	Aspergillaceae	Eukaryota	Isolated from a sandy-loam soil sample	50 m inland from Waikiki Beach, Honolulu, Hawaii	2010-JUL	PMID[22400916]
NPO31572	Aspergillus sp.	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22703109]
NPO31572	Aspergillus sp.	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23527875]
NPO31572	Aspergillus sp.	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24050204]
NPO31572	Aspergillus sp.	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25001296]
NPO31572	Aspergillus sp.	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25581396]
NPO31572	Aspergillus sp.	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26273902]
NPO41365	Aspergillus sulphureus + Isaria felina	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[29884864]
NPO31572	Aspergillus sp.	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31012585]
NPO31572	Aspergillus sp.	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[33305943]

☑ 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
IC50	2

Activity Type	# Activity
Cell Line	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT116	Cell Line	HL-60	Homo sapiens	IC50	>	10000.0	nM	PMID[23527875]
NPT111	Cell Line	K562	Homo sapiens	IC50	>	10000.0	nM	PMID[23527875]

☑ 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 NPC129277 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	302
0.1-0.2	1429
0.2-0.3	5962
0.3-0.4	11480
0.4-0.5	11434
0.5-0.6	10294
0.6-0.7	1666
0.7-0.8	111
0.8-0.85	10
0.85-0.9	3
0.9-0.95	1
0.95-1	5

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 NPC129277 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	181
0.1-0.2	543
0.2-0.3	788
0.3-0.4	1840
0.4-0.5	2651
0.5-0.6	2546
0.6-0.7	586
0.7-0.8	15
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