NPASS Compound

Structure

CID206507 OpenBabel06191715592D 31 34 0 0 1 0 0 0 0 0999 V2000 -4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 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 -0.8660 -2.5000 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 -3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 1 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 0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -2.5000 0.0000 C 0 0 0 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 -2.5981 -1.5000 0.0000 C 0 0 0 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 -3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 1 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 -5.1962 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 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 -4.3301 -1.5000 0.0000 O 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 -0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5 25 1 0 0 0 0 6 26 1 0 0 0 0 7 13 2 0 0 0 0 7 15 1 0 0 0 0 8 14 2 0 0 0 0 8 16 1 0 0 0 0 9 1 1 1 0 0 0 9 11 1 0 0 0 0 9 19 1 0 0 0 0 10 2 1 6 0 0 0 10 12 1 0 0 0 0 10 20 1 0 0 0 0 11 3 1 6 0 0 0 11 27 1 0 0 0 0 12 4 1 1 0 0 0 12 28 1 0 0 0 0 13 17 1 0 0 0 0 13 25 1 0 0 0 0 14 18 1 0 0 0 0 14 26 1 0 0 0 0 15 23 2 0 0 0 0 15 29 1 0 0 0 0 16 24 2 0 0 0 0 16 30 1 0 0 0 0 17 19 2 0 0 0 0 17 21 1 0 0 0 0 18 20 2 0 0 0 0 18 22 1 0 0 0 0 19 29 1 0 0 0 0 20 30 1 0 0 0 0 21 27 1 0 0 0 0 21 31 1 1 0 0 0 22 28 1 0 0 0 0 22 31 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	434.16
Volume:	418.136
LogP:	1.967
LogD:	2.419
LogS:	-3.847
# Rotatable Bonds:	4
TPSA:	106.57
# H-Bond Aceptor:	9
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.716
Synthetic Accessibility Score:	5.075
Fsp3:	0.545
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:	-4.863
MDCK Permeability:	4.1125385905615985e-05
Pgp-inhibitor:	0.529
Pgp-substrate:	0.9
Human Intestinal Absorption (HIA):	0.013
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.632

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.052
Plasma Protein Binding (PPB):	71.17878723144531%
Volume Distribution (VD):	1.01
Pgp-substrate:	14.929826736450195%

ADMET: Metabolism

CYP1A2-inhibitor:	0.022
CYP1A2-substrate:	0.987
CYP2C19-inhibitor:	0.165
CYP2C19-substrate:	0.924
CYP2C9-inhibitor:	0.196
CYP2C9-substrate:	0.071
CYP2D6-inhibitor:	0.03
CYP2D6-substrate:	0.323
CYP3A4-inhibitor:	0.224
CYP3A4-substrate:	0.639

ADMET: Excretion

Clearance (CL):	8.641
Half-life (T1/2):	0.204

ADMET: Toxicity

hERG Blockers:	0.009
Human Hepatotoxicity (H-HT):	0.906
Drug-inuced Liver Injury (DILI):	0.975
AMES Toxicity:	0.402
Rat Oral Acute Toxicity:	0.974
Maximum Recommended Daily Dose:	0.117
Skin Sensitization:	0.227
Carcinogencity:	0.915
Eye Corrosion:	0.003
Eye Irritation:	0.022
Respiratory Toxicity:	0.981

Download Data

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

Natural Product: NPC206507

Natural Product ID:	NPC206507
*Common Name:**	Inflatin F
IUPAC Name:	(5S,7S,8S)-4-methoxy-5-[[(5S,7S,8S)-4-methoxy-7,8-dimethyl-2-oxo-7,8-dihydro-5H-pyrano[4,3-b]pyran-5-yl]oxy]-7,8-dimethyl-7,8-dihydro-5H-pyrano[4,3-b]pyran-2-one
Synonyms:	Inflatin F
Standard InCHIKey:	CGCDOVOCJQXOOK-NVXFIYROSA-N
Standard InCHI:	InChI=1S/C22H26O9/c1-9-11(3)27-21(17-13(25-5)7-15(23)29-19(9)17)31-22-18-14(26-6)8-16(24)30-20(18)10(2)12(4)28-22/h7-12,21-22H,1-6H3/t9-,10-,11-,12-,21-,22-/m0/s1
SMILES:	C[C@H]1[C@H](C)O[C@H](c2c(cc(=O)oc12)OC)O[C@H]1c2c(cc(=O)oc2[C@@H](C)[C@H](C)O1)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1824865
PubChem CID:	53494114
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000086] Pyrans [CHEMONTID:0000481] Pyranones and derivatives

*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
NPO23794	Tolypocladium inflatum	Species	Ophiocordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21812410]
NPO23794	Tolypocladium inflatum	Species	Ophiocordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ 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	9

Activity Type	# Activity
Cell Line	5
NON-MOLECULAR	4

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell Line	A549	Homo sapiens	IC50	>	100000.0	nM	PMID[454516]
NPT1083	Cell Line	A-375	Homo sapiens	IC50	>	100000.0	nM	PMID[454516]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	>	100000.0	nM	PMID[454516]
NPT461	Cell Line	PANC-1	Homo sapiens	IC50	>	100000.0	nM	PMID[454516]
NPT941	Cell Line	HaCaT	Homo sapiens	IC50	>	100000.0	nM	PMID[454516]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	57500.0	nM	PMID[454516]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	100000.0	nM	PMID[454516]

☑ 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 NPC206507 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	382
0.1-0.2	1560
0.2-0.3	4428
0.3-0.4	10019
0.4-0.5	9454
0.5-0.6	5082
0.6-0.7	7245
0.7-0.8	4237
0.8-0.85	271
0.85-0.9	10
0.9-0.95	6
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC147621
1.0	High Similarity	NPC210258
0.8243	Intermediate Similarity	NPC178575
0.8056	Intermediate Similarity	NPC470033
0.7838	Intermediate Similarity	NPC280374
0.7746	Intermediate Similarity	NPC15193
0.7368	Intermediate Similarity	NPC470032
0.6974	Remote Similarity	NPC476589
0.6962	Remote Similarity	NPC59558
0.6923	Remote Similarity	NPC238223
0.6923	Remote Similarity	NPC477117
0.6892	Remote Similarity	NPC476585
0.6882	Remote Similarity	NPC170204
0.6875	Remote Similarity	NPC133098
0.6813	Remote Similarity	NPC327253
0.6795	Remote Similarity	NPC132286
0.679	Remote Similarity	NPC316851
0.6753	Remote Similarity	NPC476586
0.6667	Remote Similarity	NPC10080
0.6667	Remote Similarity	NPC123908
0.6667	Remote Similarity	NPC320552
0.6667	Remote Similarity	NPC25038
0.6627	Remote Similarity	NPC315552
0.6623	Remote Similarity	NPC471611
0.6575	Remote Similarity	NPC221763
0.6566	Remote Similarity	NPC197736
0.6562	Remote Similarity	NPC153559
0.6538	Remote Similarity	NPC471566
0.6538	Remote Similarity	NPC7940
0.6512	Remote Similarity	NPC271632
0.6495	Remote Similarity	NPC473307
0.6495	Remote Similarity	NPC124181
0.6494	Remote Similarity	NPC2328
0.6494	Remote Similarity	NPC476584
0.6477	Remote Similarity	NPC474028
0.6477	Remote Similarity	NPC474439
0.6463	Remote Similarity	NPC316185
0.6456	Remote Similarity	NPC469446
0.6452	Remote Similarity	NPC303451
0.6452	Remote Similarity	NPC6414
0.6447	Remote Similarity	NPC309408
0.6444	Remote Similarity	NPC470124
0.6444	Remote Similarity	NPC163606
0.6438	Remote Similarity	NPC173157
0.642	Remote Similarity	NPC151481
0.641	Remote Similarity	NPC25747
0.641	Remote Similarity	NPC148233
0.6404	Remote Similarity	NPC475714
0.6383	Remote Similarity	NPC114172
0.6383	Remote Similarity	NPC206679
0.6383	Remote Similarity	NPC471324
0.6374	Remote Similarity	NPC186332
0.6374	Remote Similarity	NPC47220
0.6364	Remote Similarity	NPC219038
0.6354	Remote Similarity	NPC291709
0.6354	Remote Similarity	NPC469543
0.6354	Remote Similarity	NPC241407
0.6351	Remote Similarity	NPC150717
0.6344	Remote Similarity	NPC242877
0.6344	Remote Similarity	NPC64913
0.6333	Remote Similarity	NPC126518
0.6329	Remote Similarity	NPC471556
0.6329	Remote Similarity	NPC471565
0.6329	Remote Similarity	NPC220766
0.6316	Remote Similarity	NPC61201
0.6316	Remote Similarity	NPC109406
0.6316	Remote Similarity	NPC159092
0.631	Remote Similarity	NPC107654
0.631	Remote Similarity	NPC470686
0.631	Remote Similarity	NPC315843
0.63	Remote Similarity	NPC471599
0.6292	Remote Similarity	NPC251026
0.6289	Remote Similarity	NPC112654
0.6286	Remote Similarity	NPC234084
0.6279	Remote Similarity	NPC10572
0.6279	Remote Similarity	NPC471225
0.6279	Remote Similarity	NPC473825
0.6279	Remote Similarity	NPC315394
0.6265	Remote Similarity	NPC181587
0.625	Remote Similarity	NPC191643
0.625	Remote Similarity	NPC294293
0.625	Remote Similarity	NPC315115
0.625	Remote Similarity	NPC124586
0.625	Remote Similarity	NPC191233
0.6237	Remote Similarity	NPC473151
0.6237	Remote Similarity	NPC233997
0.6237	Remote Similarity	NPC471057
0.6237	Remote Similarity	NPC471058
0.6234	Remote Similarity	NPC26223
0.6222	Remote Similarity	NPC473315
0.6222	Remote Similarity	NPC142111
0.622	Remote Similarity	NPC476591
0.622	Remote Similarity	NPC470693
0.622	Remote Similarity	NPC88877
0.6211	Remote Similarity	NPC476084
0.6211	Remote Similarity	NPC110072
0.6211	Remote Similarity	NPC476075
0.6203	Remote Similarity	NPC308457
0.62	Remote Similarity	NPC57586
0.62	Remote Similarity	NPC475655
0.62	Remote Similarity	NPC154132
0.62	Remote Similarity	NPC475157
0.62	Remote Similarity	NPC471637
0.62	Remote Similarity	NPC2313
0.6196	Remote Similarity	NPC471480
0.617	Remote Similarity	NPC285588
0.6163	Remote Similarity	NPC470705
0.6162	Remote Similarity	NPC90819
0.6162	Remote Similarity	NPC151093
0.6154	Remote Similarity	NPC473308
0.6154	Remote Similarity	NPC266718
0.6154	Remote Similarity	NPC475706
0.6145	Remote Similarity	NPC315285
0.6139	Remote Similarity	NPC222062
0.6129	Remote Similarity	NPC316138
0.6129	Remote Similarity	NPC74139
0.6129	Remote Similarity	NPC475186
0.6129	Remote Similarity	NPC118077
0.6129	Remote Similarity	NPC313658
0.6125	Remote Similarity	NPC182794
0.6125	Remote Similarity	NPC282760
0.6111	Remote Similarity	NPC323251
0.6105	Remote Similarity	NPC474098
0.6105	Remote Similarity	NPC475995
0.6104	Remote Similarity	NPC133600
0.61	Remote Similarity	NPC22149
0.61	Remote Similarity	NPC255677
0.61	Remote Similarity	NPC244878
0.61	Remote Similarity	NPC306344
0.6098	Remote Similarity	NPC475760
0.6098	Remote Similarity	NPC79220
0.6098	Remote Similarity	NPC313444
0.6092	Remote Similarity	NPC68156
0.6087	Remote Similarity	NPC242233
0.6087	Remote Similarity	NPC474424
0.6087	Remote Similarity	NPC471060
0.6087	Remote Similarity	NPC130030
0.6082	Remote Similarity	NPC256368
0.6082	Remote Similarity	NPC104925
0.6082	Remote Similarity	NPC469697
0.6082	Remote Similarity	NPC298973
0.6082	Remote Similarity	NPC477722
0.6081	Remote Similarity	NPC218486
0.6081	Remote Similarity	NPC159535
0.6081	Remote Similarity	NPC151761
0.6078	Remote Similarity	NPC267869
0.6078	Remote Similarity	NPC118761
0.6078	Remote Similarity	NPC197541
0.6078	Remote Similarity	NPC284929
0.6078	Remote Similarity	NPC234304
0.6076	Remote Similarity	NPC475073
0.6076	Remote Similarity	NPC210303
0.6076	Remote Similarity	NPC179087
0.6076	Remote Similarity	NPC44343
0.6076	Remote Similarity	NPC474723
0.6076	Remote Similarity	NPC474729
0.6067	Remote Similarity	NPC127295
0.6067	Remote Similarity	NPC163362
0.6064	Remote Similarity	NPC474629
0.6064	Remote Similarity	NPC196407
0.6061	Remote Similarity	NPC475332
0.6049	Remote Similarity	NPC146811
0.6042	Remote Similarity	NPC470520
0.6042	Remote Similarity	NPC472126
0.6042	Remote Similarity	NPC472125
0.6042	Remote Similarity	NPC472124
0.6042	Remote Similarity	NPC175842
0.6042	Remote Similarity	NPC32494
0.604	Remote Similarity	NPC20673
0.604	Remote Similarity	NPC298255
0.604	Remote Similarity	NPC4637
0.604	Remote Similarity	NPC98859
0.604	Remote Similarity	NPC28304
0.6026	Remote Similarity	NPC429928
0.6026	Remote Similarity	NPC79756
0.6024	Remote Similarity	NPC232812
0.6022	Remote Similarity	NPC208473
0.6022	Remote Similarity	NPC291712
0.6	Remote Similarity	NPC474913
0.6	Remote Similarity	NPC477748
0.6	Remote Similarity	NPC222244
0.6	Remote Similarity	NPC476490
0.6	Remote Similarity	NPC477457
0.6	Remote Similarity	NPC16349
0.6	Remote Similarity	NPC474440
0.6	Remote Similarity	NPC477456
0.6	Remote Similarity	NPC293044
0.6	Remote Similarity	NPC476489
0.598	Remote Similarity	NPC261117
0.598	Remote Similarity	NPC201191
0.598	Remote Similarity	NPC195510
0.598	Remote Similarity	NPC13171
0.598	Remote Similarity	NPC310804
0.5979	Remote Similarity	NPC472195
0.5979	Remote Similarity	NPC189651
0.5979	Remote Similarity	NPC475098
0.5979	Remote Similarity	NPC472196
0.5979	Remote Similarity	NPC238090
0.5978	Remote Similarity	NPC475035
0.5976	Remote Similarity	NPC194871

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 NPC206507 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	315
0.1-0.2	941
0.2-0.3	1886
0.3-0.4	2782
0.4-0.5	1895
0.5-0.6	947
0.6-0.7	290
0.7-0.8	88
0.8-0.85	6
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.6333	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.5732	Remote Similarity	NPD2685	Clinical (unspecified phase)
0.5686	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.5676	Remote Similarity	NPD6927	Phase 3
0.5652	Remote Similarity	NPD7503	Approved
0.5625	Remote Similarity	NPD1282	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