NPASS Compound

Structure

NPC48323 OpenBabel07101719252D 37 38 0 0 1 0 0 0 0 0999 V2000 -4.4529 -9.6808 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0074 3.8475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6439 -10.2686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7303 -9.8619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6258 -8.8674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7123 -8.4606 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6077 -7.4661 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6942 -7.0594 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5897 -6.0649 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3239 -5.6581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4284 -4.6636 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3420 -4.2569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4465 -3.2623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3600 -2.8556 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3601 3.3122 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 1.6984 4.7985 0.0000 C 0 0 2 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 1 0 0 0 0 0 0 0 0 0 0.0511 4.2633 0.0000 C 0 0 2 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 2.4646 -1.8611 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7202 5.0064 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7601 -0.2788 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 4.2828 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 2.3675 5.5417 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2872 2.7770 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 3.3781 -1.4543 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4112 5.9575 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 1.6555 -1.2733 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 24 1 0 0 0 0 15 21 1 0 0 0 0 15 22 1 0 0 0 0 16 23 2 0 0 0 0 16 28 1 0 0 0 0 17 20 2 0 0 0 0 17 35 1 0 0 0 0 18 28 2 0 0 0 0 18 36 1 0 0 0 0 19 2 1 6 0 0 0 19 25 1 0 0 0 0 19 30 1 0 0 0 0 20 21 1 0 0 0 0 20 29 1 0 0 0 0 21 31 1 1 0 0 0 22 25 1 0 0 0 0 22 32 1 1 0 0 0 23 26 1 0 0 0 0 23 36 1 0 0 0 0 24 33 2 0 0 0 0 24 37 1 0 0 0 0 25 34 1 1 0 0 0 26 27 1 0 0 0 0 26 37 1 6 0 0 0 27 29 2 0 0 0 0 27 35 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	524.31
Volume:	537.568
LogP:	3.818
LogD:	3.42
LogS:	-3.385
# Rotatable Bonds:	21
TPSA:	159.28
# H-Bond Aceptor:	10
# H-Bond Donor:	4
# Rings:	2
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.143
Synthetic Accessibility Score:	4.477
Fsp3:	0.741
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:	-5.374
MDCK Permeability:	3.8615948142251e-05
Pgp-inhibitor:	0.942
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.326
20% Bioavailability (F20%):	0.986
30% Bioavailability (F30%):	0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.042
Plasma Protein Binding (PPB):	94.95580291748047%
Volume Distribution (VD):	4.806
Pgp-substrate:	2.469672679901123%

ADMET: Metabolism

CYP1A2-inhibitor:	0.054
CYP1A2-substrate:	0.133
CYP2C19-inhibitor:	0.786
CYP2C19-substrate:	0.069
CYP2C9-inhibitor:	0.941
CYP2C9-substrate:	0.917
CYP2D6-inhibitor:	0.036
CYP2D6-substrate:	0.02
CYP3A4-inhibitor:	0.94
CYP3A4-substrate:	0.214

ADMET: Excretion

Clearance (CL):	5.5
Half-life (T1/2):	0.602

ADMET: Toxicity

hERG Blockers:	0.137
Human Hepatotoxicity (H-HT):	0.604
Drug-inuced Liver Injury (DILI):	0.949
AMES Toxicity:	0.022
Rat Oral Acute Toxicity:	0.833
Maximum Recommended Daily Dose:	0.704
Skin Sensitization:	0.104
Carcinogencity:	0.173
Eye Corrosion:	0.003
Eye Irritation:	0.01
Respiratory Toxicity:	0.965

Download Data

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

Natural Product: NPC48323

Natural Product ID:	NPC48323
*Common Name:**	Bengazole A
IUPAC Name:	[(S)-1,3-oxazol-5-yl-[4-[(1S,3R,4S,5R)-1,3,4,5-tetrahydroxyhexyl]-1,3-oxazol-2-yl]methyl] tetradecanoate
Synonyms:
Standard InCHIKey:	XXGWNOCDEURNQA-MXNGIANISA-N
Standard InCHI:	InChI=1S/C27H44N2O8/c1-3-4-5-6-7-8-9-10-11-12-13-14-24(33)37-26(23-16-28-18-36-23)27-29-20(17-35-27)21(31)15-22(32)25(34)19(2)30/h16-19,21-22,25-26,30-32,34H,3-15H2,1-2H3/t19-,21+,22-,25+,26+/m1/s1
SMILES:	CCCCCCCCCCCCCC(=O)O[C@H](c1occ(n1)[C@H](C[C@H]([C@H]([C@H](O)C)O)O)O)c1ocnc1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL257763
PubChem CID:	10602150
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
NPO33062	dorypleres splendens	Species	n.a.	n.a.	n.a.	Fiji	1996	PMID[18327911]
NPO40669	Jaspis cf. coricea	Strain	Ancorinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[8133293]

☑ 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
GI50	2
MIC	4
Others	17

Activity Type	# Activity
Cell Line	13
Organism	10

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT168	Cell Line	P388	Mus musculus	Activity	=	0.14	ug ml-1	PMID[533986]
NPT377	Cell Line	OVCAR-3	Homo sapiens	Activity	=	0.28	ug ml-1	PMID[533986]
NPT397	Cell Line	NCI-H460	Homo sapiens	Activity	=	0.21	ug ml-1	PMID[533986]
NPT575	Cell Line	KM-20L2	Homo sapiens	Activity	=	0.0031	ug ml-1	PMID[533986]
NPT90	Cell Line	DU-145	Homo sapiens	Activity	=	0.15	ug ml-1	PMID[533986]
NPT1081	Cell Line	BXPC-3	Homo sapiens	Activity	=	0.14	ug ml-1	PMID[533986]
NPT399	Cell Line	SF-295	Homo sapiens	Activity	=	0.19	ug ml-1	PMID[533986]
NPT407	Cell Line	COLO 205	Homo sapiens	GI50	=	181.0	nM	PMID[533987]
NPT407	Cell Line	COLO 205	Homo sapiens	TGI	=	1500.0	nM	PMID[533987]
NPT407	Cell Line	COLO 205	Homo sapiens	LC50	=	5250.0	nM	PMID[533987]
NPT373	Cell Line	SK-MEL-5	Homo sapiens	GI50	=	1130.0	nM	PMID[533987]
NPT373	Cell Line	SK-MEL-5	Homo sapiens	TGI	=	4830.0	nM	PMID[533987]
NPT373	Cell Line	SK-MEL-5	Homo sapiens	LC50	=	4830.0	nM	PMID[533987]
NPT20	Organism	Candida albicans	Candida albicans	IZ	=	9.0	mm	PMID[533988]
NPT20	Organism	Candida albicans	Candida albicans	IZ	=	50.0	mm	PMID[533989]
NPT554	Organism	Candida glabrata	Candida glabrata	IZ	=	15.0	mm	PMID[533989]
NPT187	Organism	Issatchenkia orientalis	Pichia kudriavzevii	IZ	=	35.0	mm	PMID[533989]
NPT20	Organism	Candida albicans	Candida albicans	IZ	=	15.0	mm	PMID[533989]
NPT20	Organism	Candida albicans	Candida albicans	MIC	=	1.0	ug.mL-1	PMID[533989]
NPT20	Organism	Candida albicans	Candida albicans	MIC	>	32.0	ug.mL-1	PMID[533989]

☑ 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 NPC48323 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	368
0.1-0.2	3125
0.2-0.3	15338
0.3-0.4	19441
0.4-0.5	3940
0.5-0.6	436
0.6-0.7	29
0.7-0.8	7
0.8-0.85	0
0.85-0.9	0
0.9-0.95	4
0.95-1	9

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC289029
0.9727	High Similarity	NPC258022
0.9663	High Similarity	NPC306300
0.9663	High Similarity	NPC58112
0.9663	High Similarity	NPC88938
0.9607	High Similarity	NPC46313
0.9607	High Similarity	NPC103452
0.9607	High Similarity	NPC199461
0.9399	High Similarity	NPC208297
0.9399	High Similarity	NPC224395
0.9344	High Similarity	NPC295653
0.9344	High Similarity	NPC107458
0.7233	Intermediate Similarity	NPC476829
0.7149	Intermediate Similarity	NPC476832
0.6982	Remote Similarity	NPC477219
0.6951	Remote Similarity	NPC37924
0.692	Remote Similarity	NPC325683
0.692	Remote Similarity	NPC476828
0.6872	Remote Similarity	NPC477218
0.683	Remote Similarity	NPC476830
0.6828	Remote Similarity	NPC299035
0.6828	Remote Similarity	NPC177432
0.6798	Remote Similarity	NPC168135
0.6798	Remote Similarity	NPC322800
0.6786	Remote Similarity	NPC476831
0.6786	Remote Similarity	NPC476827
0.6786	Remote Similarity	NPC476826
0.6585	Remote Similarity	NPC58001
0.6585	Remote Similarity	NPC314523
0.6583	Remote Similarity	NPC30527
0.62	Remote Similarity	NPC473833
0.6151	Remote Similarity	NPC471978
0.613	Remote Similarity	NPC314270
0.6128	Remote Similarity	NPC244536
0.6107	Remote Similarity	NPC314222
0.6107	Remote Similarity	NPC196449
0.6104	Remote Similarity	NPC326930
0.6104	Remote Similarity	NPC475301
0.608	Remote Similarity	NPC13603
0.6058	Remote Similarity	NPC477587
0.6058	Remote Similarity	NPC477589
0.604	Remote Similarity	NPC53255
0.604	Remote Similarity	NPC186452
0.604	Remote Similarity	NPC85879
0.6032	Remote Similarity	NPC472436
0.6024	Remote Similarity	NPC328928
0.6016	Remote Similarity	NPC471979
0.601	Remote Similarity	NPC211555
0.6008	Remote Similarity	NPC477588
0.6008	Remote Similarity	NPC477586
0.6008	Remote Similarity	NPC477585
0.6008	Remote Similarity	NPC477590
0.6	Remote Similarity	NPC153452
0.6	Remote Similarity	NPC12660
0.5991	Remote Similarity	NPC309919
0.5991	Remote Similarity	NPC49195
0.5975	Remote Similarity	NPC212766
0.5975	Remote Similarity	NPC289423
0.5971	Remote Similarity	NPC54983
0.5936	Remote Similarity	NPC471015
0.5935	Remote Similarity	NPC316224
0.5915	Remote Similarity	NPC90019
0.5913	Remote Similarity	NPC472435
0.5897	Remote Similarity	NPC313804
0.5897	Remote Similarity	NPC315804
0.5866	Remote Similarity	NPC258048
0.5863	Remote Similarity	NPC324619
0.5863	Remote Similarity	NPC475315
0.5826	Remote Similarity	NPC196718
0.5823	Remote Similarity	NPC475533
0.58	Remote Similarity	NPC161801
0.5769	Remote Similarity	NPC470042
0.5761	Remote Similarity	NPC102593
0.5726	Remote Similarity	NPC186351
0.572	Remote Similarity	NPC180668
0.572	Remote Similarity	NPC148896
0.572	Remote Similarity	NPC471013
0.5696	Remote Similarity	NPC316403
0.5672	Remote Similarity	NPC54066
0.5657	Remote Similarity	NPC472434
0.5652	Remote Similarity	NPC472287
0.5652	Remote Similarity	NPC472286
0.563	Remote Similarity	NPC10904
0.563	Remote Similarity	NPC165964
0.5615	Remote Similarity	NPC282346
0.5611	Remote Similarity	NPC75544

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 NPC48323 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	187
0.1-0.2	917
0.2-0.3	2560
0.3-0.4	3757
0.4-0.5	1591
0.5-0.6	137
0.6-0.7	1
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
0.621	Remote Similarity	NPD7896	Approved
0.6128	Remote Similarity	NPD4086	Phase 1
0.6101	Remote Similarity	NPD6347	Phase 2
0.6	Remote Similarity	NPD7490	Discontinued
0.5985	Remote Similarity	NPD5922	Phase 3
0.5949	Remote Similarity	NPD5640	Discontinued
0.5892	Remote Similarity	NPD7031	Phase 1
0.5873	Remote Similarity	NPD5532	Phase 2
0.5873	Remote Similarity	NPD8370	Discontinued
0.583	Remote Similarity	NPD6974	Phase 3
0.5823	Remote Similarity	NPD8356	Approved
0.5809	Remote Similarity	NPD4898	Clinical (unspecified phase)
0.5794	Remote Similarity	NPD4667	Clinical (unspecified phase)
0.5738	Remote Similarity	NPD7180	Phase 3
0.5726	Remote Similarity	NPD8430	Approved
0.5709	Remote Similarity	NPD4394	Clinical (unspecified phase)
0.5703	Remote Similarity	NPD7022	Phase 2
0.5702	Remote Similarity	NPD2433	Clinical (unspecified phase)
0.5667	Remote Similarity	NPD7547	Clinical (unspecified phase)
0.566	Remote Similarity	NPD1638	Discovery
0.563	Remote Similarity	NPD6525	Clinical (unspecified phase)
0.5615	Remote Similarity	NPD1659	Phase 1
0.561	Remote Similarity	NPD4373	Phase 2

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