NPASS Compound

Structure

NPC58112 OpenBabel07101719132D 37 38 0 0 1 0 0 0 0 0999 V2000 -11.0294 10.8239 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6958 -0.2614 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.6986 10.0808 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.3896 9.1297 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.4114 8.9218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.1024 7.9707 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.1242 7.7628 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.8152 6.8118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8371 6.6039 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5281 5.6528 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5499 5.4449 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2409 4.4938 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2628 4.2859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9537 3.3349 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9756 3.1270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1215 1.3849 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0485 0.2738 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9305 -0.2029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9945 -0.1045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4693 0.2971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3868 -1.2125 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.9305 0.7971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4013 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7395 -0.6773 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3794 1.0169 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2079 0.9781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6666 2.1759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4087 -1.4204 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.8815 -0.5119 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.6581 1.4781 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -5.0559 -1.9557 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7614 -0.8852 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3357 1.4328 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0996 -2.3715 0.0000 O 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 2.8815 1.1061 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6884 1.9680 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 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 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 27 1 0 0 0 0 16 22 1 0 0 0 0 16 26 1 0 0 0 0 17 24 1 0 0 0 0 18 22 2 0 0 0 0 18 29 1 0 0 0 0 19 23 2 0 0 0 0 19 35 1 0 0 0 0 20 29 2 0 0 0 0 20 36 1 0 0 0 0 21 2 1 1 0 0 0 21 28 1 0 0 0 0 21 31 1 0 0 0 0 22 36 1 0 0 0 0 23 25 1 0 0 0 0 23 30 1 0 0 0 0 24 28 1 0 0 0 0 24 32 1 6 0 0 0 25 17 1 1 0 0 0 25 37 1 0 0 0 0 26 30 2 0 0 0 0 26 35 1 0 0 0 0 27 33 2 0 0 0 0 27 37 1 0 0 0 0 28 34 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	522.33
Volume:	546.074
LogP:	4.915
LogD:	4.359
LogS:	-3.686
# Rotatable Bonds:	22
TPSA:	139.05
# H-Bond Aceptor:	9
# H-Bond Donor:	3
# Rings:	2
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.145
Synthetic Accessibility Score:	4.293
Fsp3:	0.75
Lipinski Rule-of-5:	Accepted
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:	-4.939
MDCK Permeability:	3.92488764191512e-05
Pgp-inhibitor:	0.465
Pgp-substrate:	0.958
Human Intestinal Absorption (HIA):	0.1
20% Bioavailability (F20%):	0.996
30% Bioavailability (F30%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.048
Plasma Protein Binding (PPB):	95.90332794189453%
Volume Distribution (VD):	5.433
Pgp-substrate:	1.7622443437576294%

ADMET: Metabolism

CYP1A2-inhibitor:	0.108
CYP1A2-substrate:	0.173
CYP2C19-inhibitor:	0.796
CYP2C19-substrate:	0.064
CYP2C9-inhibitor:	0.945
CYP2C9-substrate:	0.917
CYP2D6-inhibitor:	0.166
CYP2D6-substrate:	0.02
CYP3A4-inhibitor:	0.961
CYP3A4-substrate:	0.321

ADMET: Excretion

Clearance (CL):	8.504
Half-life (T1/2):	0.69

ADMET: Toxicity

hERG Blockers:	0.078
Human Hepatotoxicity (H-HT):	0.377
Drug-inuced Liver Injury (DILI):	0.936
AMES Toxicity:	0.024
Rat Oral Acute Toxicity:	0.814
Maximum Recommended Daily Dose:	0.577
Skin Sensitization:	0.46
Carcinogencity:	0.195
Eye Corrosion:	0.003
Eye Irritation:	0.01
Respiratory Toxicity:	0.972

Download Data

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

Natural Product: NPC58112

Natural Product ID:	NPC58112
*Common Name:**	(1R,3S,4R,5S)-3,4,5-Trihydroxy-1-(2-(Oxazol-5-Ylmethyl)Oxazol-4-Yl)Hexyl Pentadecanoate
IUPAC Name:	[(1R,3S,4R,5S)-3,4,5-trihydroxy-1-[2-(1,3-oxazol-5-ylmethyl)-1,3-oxazol-4-yl]hexyl] pentadecanoate
Synonyms:
Standard InCHIKey:	PLOFEGFCNJWYDI-SRDXBBKJSA-N
Standard InCHI:	InChI=1S/C28H46N2O7/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-27(33)37-25(17-24(32)28(34)21(2)31)23-19-35-26(30-23)16-22-18-29-20-36-22/h18-21,24-25,28,31-32,34H,3-17H2,1-2H3/t21-,24-,25+,28+/m0/s1
SMILES:	CCCCCCCCCCCCCCC(=O)O[C@H](C[C@@H]([C@@H]([C@H](C)O)O)O)c1coc(Cc2cnco2)n1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL491710
PubChem CID:	487129
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000436] Azoles [CHEMONTID:0000083] Oxazoles [CHEMONTID:0002638] 2,4-disubstituted oxazoles

*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
NPO32703	pachastrissa sp.	Species	Calthropellidae	Eukaryota	n.a.	n.a.	n.a.	PMID[10346943]
NPO32703	pachastrissa sp.	Species	Calthropellidae	Eukaryota	n.a.	n.a.	n.a.	PMID[12398554]

☑ 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
MIC	1

Activity Type	# Activity
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20	Organism	Candida albicans	Candida albicans	MIC	=	0.8	ug.mL-1	PMID[488182]

☑ 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 NPC58112 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	334
0.1-0.2	3026
0.2-0.3	15883
0.3-0.4	19097
0.4-0.5	3856
0.5-0.6	447
0.6-0.7	32
0.7-0.8	9
0.8-0.85	0
0.85-0.9	0
0.9-0.95	3
0.95-1	10

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC88938
1.0	High Similarity	NPC306300
0.9718	High Similarity	NPC224395
0.9718	High Similarity	NPC208297
0.9713	High Similarity	NPC199461
0.9713	High Similarity	NPC46313
0.9713	High Similarity	NPC103452
0.9663	High Similarity	NPC48323
0.9663	High Similarity	NPC289029
0.9441	High Similarity	NPC107458
0.9441	High Similarity	NPC295653
0.9399	High Similarity	NPC258022
0.7108	Intermediate Similarity	NPC476829
0.7097	Intermediate Similarity	NPC477219
0.7064	Intermediate Similarity	NPC37924
0.7032	Intermediate Similarity	NPC325683
0.7032	Intermediate Similarity	NPC476828
0.6937	Remote Similarity	NPC299035
0.6937	Remote Similarity	NPC177432
0.6906	Remote Similarity	NPC477218
0.6906	Remote Similarity	NPC168135
0.6906	Remote Similarity	NPC322800
0.6895	Remote Similarity	NPC476831
0.6895	Remote Similarity	NPC476827
0.6895	Remote Similarity	NPC476826
0.6878	Remote Similarity	NPC476832
0.6864	Remote Similarity	NPC476830
0.6701	Remote Similarity	NPC30527
0.67	Remote Similarity	NPC314523
0.67	Remote Similarity	NPC58001
0.6224	Remote Similarity	NPC186452
0.6193	Remote Similarity	NPC211555
0.6187	Remote Similarity	NPC196449
0.6187	Remote Similarity	NPC314222
0.6181	Remote Similarity	NPC12660
0.615	Remote Similarity	NPC54983
0.6079	Remote Similarity	NPC309919
0.6078	Remote Similarity	NPC244536
0.6076	Remote Similarity	NPC477587
0.6076	Remote Similarity	NPC477589
0.6048	Remote Similarity	NPC472436
0.6025	Remote Similarity	NPC477590
0.6025	Remote Similarity	NPC477585
0.6025	Remote Similarity	NPC477586
0.6025	Remote Similarity	NPC477588
0.6024	Remote Similarity	NPC473833
0.6018	Remote Similarity	NPC153452
0.6009	Remote Similarity	NPC49195
0.5991	Remote Similarity	NPC289423
0.5991	Remote Similarity	NPC212766
0.5976	Remote Similarity	NPC471978
0.5975	Remote Similarity	NPC196718
0.5931	Remote Similarity	NPC90019
0.5927	Remote Similarity	NPC475301
0.5927	Remote Similarity	NPC472435
0.5927	Remote Similarity	NPC326930
0.5913	Remote Similarity	NPC315804
0.5913	Remote Similarity	NPC313804
0.5907	Remote Similarity	NPC102593
0.5904	Remote Similarity	NPC13603
0.5885	Remote Similarity	NPC316224
0.5878	Remote Similarity	NPC161801
0.587	Remote Similarity	NPC314270
0.5863	Remote Similarity	NPC53255
0.5863	Remote Similarity	NPC85879
0.585	Remote Similarity	NPC328928
0.5843	Remote Similarity	NPC470042
0.5843	Remote Similarity	NPC471979
0.5823	Remote Similarity	NPC471015
0.5754	Remote Similarity	NPC258048
0.5738	Remote Similarity	NPC186351
0.5732	Remote Similarity	NPC471013
0.5732	Remote Similarity	NPC148896
0.5732	Remote Similarity	NPC180668
0.5708	Remote Similarity	NPC316403
0.5686	Remote Similarity	NPC282346
0.5685	Remote Similarity	NPC324619
0.5685	Remote Similarity	NPC475315
0.5684	Remote Similarity	NPC54066
0.5668	Remote Similarity	NPC472434
0.5664	Remote Similarity	NPC472286
0.5664	Remote Similarity	NPC472287
0.5645	Remote Similarity	NPC58209
0.5645	Remote Similarity	NPC475533
0.564	Remote Similarity	NPC10904
0.5622	Remote Similarity	NPC75544
0.5605	Remote Similarity	NPC220408
0.5603	Remote Similarity	NPC209981

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 NPC58112 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	183
0.1-0.2	878
0.2-0.3	2483
0.3-0.4	3817
0.4-0.5	1639
0.5-0.6	148
0.6-0.7	2
0.7-0.8	0
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
0.6233	Remote Similarity	NPD7896	Approved
0.6197	Remote Similarity	NPD6347	Phase 2
0.6093	Remote Similarity	NPD7490	Discontinued
0.6078	Remote Similarity	NPD4086	Phase 1
0.5983	Remote Similarity	NPD6974	Phase 3
0.5951	Remote Similarity	NPD5532	Phase 2
0.5887	Remote Similarity	NPD7180	Phase 3
0.5875	Remote Similarity	NPD5922	Phase 3
0.584	Remote Similarity	NPD7031	Phase 1
0.5837	Remote Similarity	NPD8356	Approved
0.5823	Remote Similarity	NPD8370	Discontinued
0.5823	Remote Similarity	NPD4898	Clinical (unspecified phase)
0.5812	Remote Similarity	NPD7547	Clinical (unspecified phase)
0.5783	Remote Similarity	NPD2433	Clinical (unspecified phase)
0.5763	Remote Similarity	NPD5640	Discontinued
0.5756	Remote Similarity	NPD1659	Phase 1
0.5738	Remote Similarity	NPD8430	Approved
0.5732	Remote Similarity	NPD7284	Clinical (unspecified phase)
0.5703	Remote Similarity	NPD6525	Clinical (unspecified phase)
0.5702	Remote Similarity	NPD7853	Phase 2
0.5697	Remote Similarity	NPD6252	Clinical (unspecified phase)
0.5671	Remote Similarity	NPD4667	Clinical (unspecified phase)
0.5671	Remote Similarity	NPD6169	Phase 1
0.5638	Remote Similarity	NPD3006	Discontinued
0.5633	Remote Similarity	NPD7886	Phase 2
0.5633	Remote Similarity	NPD7885	Phase 2
0.5608	Remote Similarity	NPD3801	Clinical (unspecified phase)
0.56	Remote Similarity	NPD2779	Approved

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