NPASS Compound

Structure

NPC199461 OpenBabel07101718302D 37 38 0 0 1 0 0 0 0 0999 V2000 -16.0616 0.6052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9344 2.2418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -15.7526 -0.3459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -14.7744 -0.5538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -14.1053 0.1893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -13.1271 -0.0186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.4580 0.7246 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.4799 0.5167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.8107 1.2598 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.8326 1.0519 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.1634 1.7950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1853 1.5871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5162 2.3303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5380 2.1224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8689 2.8655 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7601 -0.2788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2872 2.7770 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5396 -0.3720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5878 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8761 1.2106 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2435 3.1928 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.6736 0.1280 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.6180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3090 2.5691 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.5962 3.7281 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9511 0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8907 2.6576 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5743 3.9360 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2828 0.2971 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 1.3090 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.3601 3.3122 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9271 4.4712 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5817 1.7065 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8833 4.8870 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 -4.2216 3.4007 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 17 25 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 6 0 0 0 21 28 1 0 0 0 0 21 37 1 0 0 0 0 22 36 1 0 0 0 0 23 24 1 0 0 0 0 23 30 1 0 0 0 0 24 31 1 1 0 0 0 25 28 1 0 0 0 0 25 32 1 1 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 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	522.33
Volume:	546.074
LogP:	4.903
LogD:	4.225
LogS:	-3.482
# 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:	4.323
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:	-4.867
MDCK Permeability:	3.356182060088031e-05
Pgp-inhibitor:	0.49
Pgp-substrate:	0.893
Human Intestinal Absorption (HIA):	0.114
20% Bioavailability (F20%):	0.988
30% Bioavailability (F30%):	0.98

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.052
Plasma Protein Binding (PPB):	95.1915054321289%
Volume Distribution (VD):	5.052
Pgp-substrate:	1.0578203201293945%

ADMET: Metabolism

CYP1A2-inhibitor:	0.162
CYP1A2-substrate:	0.146
CYP2C19-inhibitor:	0.804
CYP2C19-substrate:	0.057
CYP2C9-inhibitor:	0.95
CYP2C9-substrate:	0.884
CYP2D6-inhibitor:	0.335
CYP2D6-substrate:	0.017
CYP3A4-inhibitor:	0.97
CYP3A4-substrate:	0.337

ADMET: Excretion

Clearance (CL):	9.368
Half-life (T1/2):	0.644

ADMET: Toxicity

hERG Blockers:	0.07
Human Hepatotoxicity (H-HT):	0.368
Drug-inuced Liver Injury (DILI):	0.925
AMES Toxicity:	0.022
Rat Oral Acute Toxicity:	0.658
Maximum Recommended Daily Dose:	0.886
Skin Sensitization:	0.649
Carcinogencity:	0.323
Eye Corrosion:	0.003
Eye Irritation:	0.01
Respiratory Toxicity:	0.975

Download Data

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

Natural Product: NPC199461

Natural Product ID:	NPC199461
*Common Name:**	(2S,3S,4S,6R)-3,4,6-Trihydroxy-6-(2-(Oxazol-5-Ylmethyl)Oxazol-4-Yl)Hexan-2-Yl Pentadecanoate
IUPAC Name:	[(2S,3S,4S,6R)-3,4,6-trihydroxy-6-[2-(1,3-oxazol-5-ylmethyl)-1,3-oxazol-4-yl]hexan-2-yl] pentadecanoate
Synonyms:
Standard InCHIKey:	ZXNZLZRRNGBRNT-HAUPEQAHSA-N
Standard InCHI:	InChI=1S/C28H46N2O7/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-27(33)37-21(2)28(34)25(32)17-24(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@H]([C@H](C[C@H](c1coc(n1)Cc1cnco1)O)O)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL491373
PubChem CID:	5482491
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[532705]

☑ 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 NPC199461 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	326
0.1-0.2	2873
0.2-0.3	16381
0.3-0.4	18966
0.4-0.5	3726
0.5-0.6	374
0.6-0.7	38
0.7-0.8	0
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	NPC46313
1.0	High Similarity	NPC103452
0.9716	High Similarity	NPC295653
0.9716	High Similarity	NPC107458
0.9713	High Similarity	NPC58112
0.9713	High Similarity	NPC88938
0.9713	High Similarity	NPC306300
0.9607	High Similarity	NPC48323
0.9607	High Similarity	NPC289029
0.9441	High Similarity	NPC208297
0.9441	High Similarity	NPC224395
0.9344	High Similarity	NPC258022
0.6895	Remote Similarity	NPC477219
0.6893	Remote Similarity	NPC476829
0.6864	Remote Similarity	NPC37924
0.6833	Remote Similarity	NPC476832
0.6833	Remote Similarity	NPC325683
0.6833	Remote Similarity	NPC476828
0.6786	Remote Similarity	NPC477218
0.6742	Remote Similarity	NPC476830
0.6741	Remote Similarity	NPC299035
0.6741	Remote Similarity	NPC177432
0.6711	Remote Similarity	NPC168135
0.6711	Remote Similarity	NPC322800
0.6697	Remote Similarity	NPC476827
0.6697	Remote Similarity	NPC476826
0.6697	Remote Similarity	NPC476831
0.665	Remote Similarity	NPC58001
0.665	Remote Similarity	NPC314523
0.6564	Remote Similarity	NPC30527
0.6245	Remote Similarity	NPC244536
0.6106	Remote Similarity	NPC49195
0.6091	Remote Similarity	NPC186452
0.6085	Remote Similarity	NPC196449
0.6085	Remote Similarity	NPC314222
0.6061	Remote Similarity	NPC211555
0.605	Remote Similarity	NPC12660
0.602	Remote Similarity	NPC54983
0.6009	Remote Similarity	NPC313804
0.6009	Remote Similarity	NPC315804
0.5966	Remote Similarity	NPC477587
0.5966	Remote Similarity	NPC477589
0.5965	Remote Similarity	NPC309919
0.5944	Remote Similarity	NPC472436
0.592	Remote Similarity	NPC473833
0.5917	Remote Similarity	NPC477590
0.5917	Remote Similarity	NPC477588
0.5917	Remote Similarity	NPC477585
0.5917	Remote Similarity	NPC477586
0.5903	Remote Similarity	NPC153452
0.5895	Remote Similarity	NPC314270
0.588	Remote Similarity	NPC212766
0.588	Remote Similarity	NPC289423
0.5873	Remote Similarity	NPC471978
0.5844	Remote Similarity	NPC316224
0.583	Remote Similarity	NPC186351
0.5823	Remote Similarity	NPC326930
0.5823	Remote Similarity	NPC475301
0.5823	Remote Similarity	NPC472435
0.5819	Remote Similarity	NPC90019
0.5804	Remote Similarity	NPC316403
0.58	Remote Similarity	NPC13603
0.5798	Remote Similarity	NPC196718
0.5794	Remote Similarity	NPC75544
0.5772	Remote Similarity	NPC161801
0.576	Remote Similarity	NPC85879
0.576	Remote Similarity	NPC53255
0.5748	Remote Similarity	NPC328928
0.5742	Remote Similarity	NPC470042
0.5742	Remote Similarity	NPC471979
0.5732	Remote Similarity	NPC102593
0.572	Remote Similarity	NPC471015
0.5714	Remote Similarity	NPC258048
0.5641	Remote Similarity	NPC54066
0.5628	Remote Similarity	NPC180668
0.5628	Remote Similarity	NPC471013
0.5628	Remote Similarity	NPC148896
0.5619	Remote Similarity	NPC472287
0.5619	Remote Similarity	NPC472286
0.5619	Remote Similarity	NPC475455
0.56	Remote Similarity	NPC50274

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 NPC199461 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	182
0.1-0.2	847
0.2-0.3	2564
0.3-0.4	3872
0.4-0.5	1559
0.5-0.6	123
0.6-0.7	3
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
0.6338	Remote Similarity	NPD7896	Approved
0.6303	Remote Similarity	NPD6347	Phase 2
0.6245	Remote Similarity	NPD4086	Phase 1
0.6197	Remote Similarity	NPD7490	Discontinued
0.5976	Remote Similarity	NPD8370	Discontinued
0.5931	Remote Similarity	NPD8356	Approved
0.5847	Remote Similarity	NPD5532	Phase 2
0.583	Remote Similarity	NPD8430	Approved
0.5801	Remote Similarity	NPD6974	Phase 3
0.5781	Remote Similarity	NPD4898	Clinical (unspecified phase)
0.5775	Remote Similarity	NPD5922	Phase 3
0.5732	Remote Similarity	NPD7031	Phase 1
0.572	Remote Similarity	NPD5640	Discontinued
0.5708	Remote Similarity	NPD7180	Phase 3
0.5671	Remote Similarity	NPD2433	Clinical (unspecified phase)
0.5636	Remote Similarity	NPD7547	Clinical (unspecified phase)
0.56	Remote Similarity	NPD6525	Clinical (unspecified phase)

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