NPASS Compound

Structure

NPC484727 OpenBabel06302216212D 30 30 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 2 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 1 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 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5981 -2.5000 0.0000 C 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 -2.5981 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -8.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -11.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -12.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -12.0000 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 0.0000 -4.0000 0.0000 C 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 2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 O 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 7 1 0 0 0 0 3 4 1 0 0 0 0 3 30 1 1 0 0 0 4 5 1 0 0 0 0 4 29 1 1 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 6 0 0 0 9 8 1 1 0 0 0 9 10 1 0 0 0 0 9 26 1 0 0 0 0 10 11 1 1 0 0 0 10 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 13 15 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 19 20 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 23 25 1 0 0 0 0 26 27 1 0 0 0 0 26 28 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	420.25
Volume:	452.026
LogP:	2.694
LogD:	2.206
LogS:	-3.929
# Rotatable Bonds:	10
TPSA:	96.22
# H-Bond Aceptor:	6
# H-Bond Donor:	3
# Rings:	1
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.368
Synthetic Accessibility Score:	4.781
Fsp3:	0.542
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.072
MDCK Permeability:	8.353588782483712e-06
Pgp-inhibitor:	0.001
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.025
20% Bioavailability (F20%):	0.166
30% Bioavailability (F30%):	0.528

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.039
Plasma Protein Binding (PPB):	87.6535415649414%
Volume Distribution (VD):	0.566
Pgp-substrate:	5.792948246002197%

ADMET: Metabolism

CYP1A2-inhibitor:	0.189
CYP1A2-substrate:	0.081
CYP2C19-inhibitor:	0.092
CYP2C19-substrate:	0.156
CYP2C9-inhibitor:	0.185
CYP2C9-substrate:	0.996
CYP2D6-inhibitor:	0.72
CYP2D6-substrate:	0.9
CYP3A4-inhibitor:	0.182
CYP3A4-substrate:	0.159

ADMET: Excretion

Clearance (CL):	1.678
Half-life (T1/2):	0.407

ADMET: Toxicity

hERG Blockers:	0.118
Human Hepatotoxicity (H-HT):	0.627
Drug-inuced Liver Injury (DILI):	0.81
AMES Toxicity:	0.503
Rat Oral Acute Toxicity:	0.036
Maximum Recommended Daily Dose:	0.718
Skin Sensitization:	0.804
Carcinogencity:	0.297
Eye Corrosion:	0.035
Eye Irritation:	0.188
Respiratory Toxicity:	0.92

Download Data

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

Natural Product: NPC484727

Natural Product ID:	NPC484727
*Common Name:**	ZOGIGJKRUBEBDV-DYONNZCLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZOGIGJKRUBEBDV-DYONNZCLSA-N
Standard InCHI:	InChI=1S/C24H36O6/c1-16(2)24(30-22-15-20(25)23(28)19(5)29-22)18(4)14-17(3)12-10-8-6-7-9-11-13-21(26)27/h6-14,16,18-20,22-25,28H,15H2,1-5H3,(H,26,27)/b8-6+,9-7+,12-10+,13-11+,17-14+/t18-,19-,20+,22+,23-,24+/m1/s1
SMILES:	CC(C)[C@@H]([C@H](C)/C=C(C)/C=C/C=C/C=C/C=C/C(=O)O)O[C@H]1C[C@@H]([C@@H]([C@@H](C)O1)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0000262] Fatty acids and conjugates [CHEMONTID:0002949] Long-chain fatty acids

*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
NPO40628	Streptomyces tendae KMC006	Strain	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[28845982]
NPO40523	Gordonia sp. KMC005	Strain	Gordoniaceae	Bacteria	n.a.	n.a.	n.a.	PMID[28845982]
NPO41433	Gordonia sp. KMC005 + Streptomyces tendae KMC006	Strain	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[28845982]
NPO41549	Streptomyces tendae KMC006 + Gordonia sp. KMC005	Strain	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[28845982]

☑ 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
Others	2

Activity Type	# Activity
Organism	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT3721	Organism	Enterococcus hirae	Enterococcus hirae	IZ	=	1.5	mm	PMID[28845982]
NPT729	Organism	Micrococcus luteus	Micrococcus luteus	IZ	=	2.5	mm	PMID[28845982]

☑ 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 NPC484727 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	171
0.1-0.2	1338
0.2-0.3	5198
0.3-0.4	12688
0.4-0.5	13161
0.5-0.6	7683
0.6-0.7	2105
0.7-0.8	313
0.8-0.85	23
0.85-0.9	12
0.9-0.95	4
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 NPC484727 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	146
0.1-0.2	1563
0.2-0.3	4115
0.3-0.4	2319
0.4-0.5	749
0.5-0.6	220
0.6-0.7	35
0.7-0.8	3
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