NPASS Compound

Structure

NPC245002 OpenBabel07101718292D 22 22 0 0 1 0 0 0 0 0999 V2000 1.5332 6.2222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3360 1.1023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1748 5.2886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8042 4.5115 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7918 4.6679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4212 3.8908 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4088 4.0472 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0382 3.2700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6798 2.3365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3091 1.5593 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9508 0.6257 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9631 0.4693 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6047 -0.4643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6170 -0.6207 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -1.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9877 0.1564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3090 -0.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3090 -0.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.2601 -1.2601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6502 0.9368 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 1 3 1 0 0 0 0 2 21 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 2 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 14 16 1 0 0 0 0 15 17 2 0 0 0 0 15 18 1 0 0 0 0 17 19 1 0 0 0 0 18 20 2 0 0 0 0 18 22 1 0 0 0 0 19 16 1 1 0 0 0 19 21 1 0 0 0 0 19 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	304.2
Volume:	341.812
LogP:	2.648
LogD:	3.096
LogS:	-3.332
# Rotatable Bonds:	11
TPSA:	35.53
# H-Bond Aceptor:	3
# H-Bond Donor:	0
# Rings:	1
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.31
Synthetic Accessibility Score:	3.844
Fsp3:	0.526
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.839
MDCK Permeability:	0.00010012651182478294
Pgp-inhibitor:	0.0
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.024
20% Bioavailability (F20%):	0.998
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.225
Plasma Protein Binding (PPB):	97.2537612915039%
Volume Distribution (VD):	1.969
Pgp-substrate:	1.2267136573791504%

ADMET: Metabolism

CYP1A2-inhibitor:	0.284
CYP1A2-substrate:	0.747
CYP2C19-inhibitor:	0.798
CYP2C19-substrate:	0.74
CYP2C9-inhibitor:	0.572
CYP2C9-substrate:	0.306
CYP2D6-inhibitor:	0.794
CYP2D6-substrate:	0.623
CYP3A4-inhibitor:	0.931
CYP3A4-substrate:	0.397

ADMET: Excretion

Clearance (CL):	5.698
Half-life (T1/2):	0.89

ADMET: Toxicity

hERG Blockers:	0.061
Human Hepatotoxicity (H-HT):	0.234
Drug-inuced Liver Injury (DILI):	0.007
AMES Toxicity:	0.865
Rat Oral Acute Toxicity:	0.008
Maximum Recommended Daily Dose:	0.613
Skin Sensitization:	0.976
Carcinogencity:	0.76
Eye Corrosion:	0.024
Eye Irritation:	0.211
Respiratory Toxicity:	0.881

Download Data

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

Natural Product: NPC245002

Natural Product ID:	NPC245002
*Common Name:**	Homaxinolide A
IUPAC Name:	(5S)-5-methoxy-5-[(2Z,5Z,8Z)-tetradeca-2,5,8-trienyl]furan-2-one
Synonyms:
Standard InCHIKey:	CNMJVHJGBMQNPN-VXAMVLJISA-N
Standard InCHI:	InChI=1S/C19H28O3/c1-3-4-5-6-7-8-9-10-11-12-13-14-16-19(21-2)17-15-18(20)22-19/h7-8,10-11,13-15,17H,3-6,9,12,16H2,1-2H3/b8-7-,11-10-,14-13-/t19-/m0/s1
SMILES:	CCCCC/C=CC/C=CC/C=CC[C@@]1(OC)C=CC(=O)O1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL461184
PubChem CID:	10040732
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000254] Ethers [CHEMONTID:0001656] Acetals [CHEMONTID:0004472] Ketals

*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
NPO33466	Homaxinella	Genus		Eukaryota	n.a.	n.a.	n.a.	PMID[15104515]

☑ 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
ED50	5

Activity Type	# Activity
Cell Line	5

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell Line	A549	Homo sapiens	ED50	=	10.1	ug ml-1	PMID[537949]
NPT146	Cell Line	SK-OV-3	Homo sapiens	ED50	=	16.1	ug ml-1	PMID[537949]
NPT147	Cell Line	SK-MEL-2	Homo sapiens	ED50	=	2.7	ug ml-1	PMID[537949]
NPT574	Cell Line	XF498	Homo sapiens	ED50	=	9.9	ug ml-1	PMID[537949]
NPT148	Cell Line	HCT-15	Homo sapiens	ED50	=	8.9	ug ml-1	PMID[537949]

☑ 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 NPC245002 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	152
0.1-0.2	5319
0.2-0.3	19846
0.3-0.4	11530
0.4-0.5	4092
0.5-0.6	1414
0.6-0.7	288
0.7-0.8	52
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
0.9615	High Similarity	NPC159535
0.9615	High Similarity	NPC151761
0.8929	High Similarity	NPC474084
0.8033	Intermediate Similarity	NPC210303
0.8033	Intermediate Similarity	NPC44343
0.8033	Intermediate Similarity	NPC179087
0.7759	Intermediate Similarity	NPC478117
0.7705	Intermediate Similarity	NPC26223
0.7593	Intermediate Similarity	NPC128280
0.7581	Intermediate Similarity	NPC151648
0.7541	Intermediate Similarity	NPC22897
0.7541	Intermediate Similarity	NPC159650
0.7541	Intermediate Similarity	NPC286189
0.7538	Intermediate Similarity	NPC225272
0.75	Intermediate Similarity	NPC236338
0.75	Intermediate Similarity	NPC275316
0.75	Intermediate Similarity	NPC15789
0.7407	Intermediate Similarity	NPC270706
0.7385	Intermediate Similarity	NPC248125
0.7344	Intermediate Similarity	NPC148233
0.7344	Intermediate Similarity	NPC308457
0.7344	Intermediate Similarity	NPC25747
0.7302	Intermediate Similarity	NPC26810
0.7288	Intermediate Similarity	NPC478120
0.7273	Intermediate Similarity	NPC203335
0.7273	Intermediate Similarity	NPC197467
0.7241	Intermediate Similarity	NPC106531
0.7231	Intermediate Similarity	NPC182794
0.7231	Intermediate Similarity	NPC220766
0.7231	Intermediate Similarity	NPC133904
0.7231	Intermediate Similarity	NPC470688
0.7213	Intermediate Similarity	NPC129150
0.7213	Intermediate Similarity	NPC294938
0.7188	Intermediate Similarity	NPC473737
0.717	Intermediate Similarity	NPC57923
0.7164	Intermediate Similarity	NPC218477
0.7121	Intermediate Similarity	NPC124586
0.7121	Intermediate Similarity	NPC276299
0.7121	Intermediate Similarity	NPC191233
0.7121	Intermediate Similarity	NPC146811
0.7097	Intermediate Similarity	NPC254095
0.7097	Intermediate Similarity	NPC223679
0.7091	Intermediate Similarity	NPC26600
0.7091	Intermediate Similarity	NPC47946
0.7083	Intermediate Similarity	NPC10572
0.7059	Intermediate Similarity	NPC470693
0.7049	Intermediate Similarity	NPC86948
0.7	Intermediate Similarity	NPC269615
0.6984	Remote Similarity	NPC478095
0.6984	Remote Similarity	NPC82465
0.6984	Remote Similarity	NPC133600
0.697	Remote Similarity	NPC96414
0.697	Remote Similarity	NPC282760
0.697	Remote Similarity	NPC19769
0.6935	Remote Similarity	NPC293437
0.6935	Remote Similarity	NPC212730
0.6935	Remote Similarity	NPC471279
0.6935	Remote Similarity	NPC265551
0.6935	Remote Similarity	NPC471277
0.6935	Remote Similarity	NPC135863
0.6935	Remote Similarity	NPC249850
0.6923	Remote Similarity	NPC474774
0.6923	Remote Similarity	NPC475073
0.6923	Remote Similarity	NPC68110
0.6923	Remote Similarity	NPC474723
0.6923	Remote Similarity	NPC474729
0.6912	Remote Similarity	NPC475760
0.6912	Remote Similarity	NPC470256
0.6912	Remote Similarity	NPC474823
0.6885	Remote Similarity	NPC474913
0.6875	Remote Similarity	NPC79756
0.6875	Remote Similarity	NPC130953
0.6866	Remote Similarity	NPC201356
0.6825	Remote Similarity	NPC21946
0.6825	Remote Similarity	NPC478096
0.6825	Remote Similarity	NPC189700
0.6812	Remote Similarity	NPC475004
0.6812	Remote Similarity	NPC265574
0.6812	Remote Similarity	NPC151481
0.6774	Remote Similarity	NPC230296
0.6765	Remote Similarity	NPC21998
0.6765	Remote Similarity	NPC122627
0.6765	Remote Similarity	NPC472266
0.6765	Remote Similarity	NPC194871
0.6761	Remote Similarity	NPC287878
0.6761	Remote Similarity	NPC476490
0.6761	Remote Similarity	NPC476489
0.6761	Remote Similarity	NPC474705
0.6724	Remote Similarity	NPC135698
0.6724	Remote Similarity	NPC15912
0.6721	Remote Similarity	NPC151923
0.6721	Remote Similarity	NPC9611
0.6719	Remote Similarity	NPC222852
0.6719	Remote Similarity	NPC97570
0.6719	Remote Similarity	NPC474267
0.6719	Remote Similarity	NPC302564
0.6716	Remote Similarity	NPC131174
0.6714	Remote Similarity	NPC476037
0.6714	Remote Similarity	NPC476012
0.6667	Remote Similarity	NPC132243
0.6667	Remote Similarity	NPC276290
0.6667	Remote Similarity	NPC474658
0.6667	Remote Similarity	NPC217940
0.662	Remote Similarity	NPC293114
0.662	Remote Similarity	NPC475762
0.662	Remote Similarity	NPC316185
0.662	Remote Similarity	NPC84038
0.662	Remote Similarity	NPC186531
0.6618	Remote Similarity	NPC37382
0.6615	Remote Similarity	NPC471278
0.6615	Remote Similarity	NPC98519
0.661	Remote Similarity	NPC27264
0.6604	Remote Similarity	NPC147824
0.6571	Remote Similarity	NPC476591
0.6571	Remote Similarity	NPC475982
0.6571	Remote Similarity	NPC232812
0.6571	Remote Similarity	NPC88877
0.6567	Remote Similarity	NPC475618
0.6567	Remote Similarity	NPC470808
0.6567	Remote Similarity	NPC114464
0.6557	Remote Similarity	NPC477781
0.6557	Remote Similarity	NPC477780
0.6552	Remote Similarity	NPC90490
0.6528	Remote Similarity	NPC16349
0.6528	Remote Similarity	NPC284006
0.6528	Remote Similarity	NPC329890
0.6528	Remote Similarity	NPC185186
0.6528	Remote Similarity	NPC327383
0.6528	Remote Similarity	NPC222244
0.6528	Remote Similarity	NPC329914
0.6508	Remote Similarity	NPC472808
0.6508	Remote Similarity	NPC324224
0.6508	Remote Similarity	NPC96663
0.6508	Remote Similarity	NPC221763
0.6508	Remote Similarity	NPC150717
0.65	Remote Similarity	NPC148056
0.6486	Remote Similarity	NPC123360
0.6486	Remote Similarity	NPC4509
0.6481	Remote Similarity	NPC281043
0.6481	Remote Similarity	NPC297608
0.6481	Remote Similarity	NPC123357
0.6479	Remote Similarity	NPC64234
0.6479	Remote Similarity	NPC37929
0.6479	Remote Similarity	NPC469660
0.6471	Remote Similarity	NPC471565
0.6471	Remote Similarity	NPC470123
0.6471	Remote Similarity	NPC273600
0.6471	Remote Similarity	NPC475110
0.6471	Remote Similarity	NPC471556
0.6471	Remote Similarity	NPC471566
0.6441	Remote Similarity	NPC207815
0.6441	Remote Similarity	NPC82446
0.6438	Remote Similarity	NPC259599
0.6438	Remote Similarity	NPC107654
0.6438	Remote Similarity	NPC294434
0.6438	Remote Similarity	NPC476355
0.6438	Remote Similarity	NPC117746
0.6438	Remote Similarity	NPC470686
0.6438	Remote Similarity	NPC15499
0.6438	Remote Similarity	NPC315843
0.6438	Remote Similarity	NPC474758
0.6429	Remote Similarity	NPC63873
0.6418	Remote Similarity	NPC155849
0.6415	Remote Similarity	NPC226511
0.641	Remote Similarity	NPC474959
0.641	Remote Similarity	NPC310450
0.641	Remote Similarity	NPC475046
0.641	Remote Similarity	NPC251026
0.641	Remote Similarity	NPC11383
0.6406	Remote Similarity	NPC474825
0.6406	Remote Similarity	NPC44542
0.6406	Remote Similarity	NPC223804
0.6393	Remote Similarity	NPC191643
0.6393	Remote Similarity	NPC151919
0.6389	Remote Similarity	NPC163003
0.6389	Remote Similarity	NPC257618
0.6379	Remote Similarity	NPC308331
0.6377	Remote Similarity	NPC475555
0.6377	Remote Similarity	NPC475675
0.6364	Remote Similarity	NPC229252
0.6364	Remote Similarity	NPC299730
0.6364	Remote Similarity	NPC221250
0.6364	Remote Similarity	NPC309408
0.6364	Remote Similarity	NPC143857
0.6351	Remote Similarity	NPC329852
0.6351	Remote Similarity	NPC329826
0.6351	Remote Similarity	NPC285840
0.6351	Remote Similarity	NPC469414
0.6351	Remote Similarity	NPC327041
0.6351	Remote Similarity	NPC260396
0.6349	Remote Similarity	NPC173157
0.6329	Remote Similarity	NPC286770
0.6329	Remote Similarity	NPC229799
0.6329	Remote Similarity	NPC30502
0.6329	Remote Similarity	NPC284472
0.6329	Remote Similarity	NPC142111
0.6329	Remote Similarity	NPC473315
0.6324	Remote Similarity	NPC477457
0.6324	Remote Similarity	NPC477456
0.6316	Remote Similarity	NPC12907

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 NPC245002 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	136
0.1-0.2	4273
0.2-0.3	3861
0.3-0.4	726
0.4-0.5	111
0.5-0.6	35
0.6-0.7	8
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
0.678	Remote Similarity	NPD6927	Phase 3
0.6471	Remote Similarity	NPD2685	Clinical (unspecified phase)
0.6441	Remote Similarity	NPD4220	Pre-registration
0.6316	Remote Similarity	NPD6097	Approved
0.6316	Remote Similarity	NPD6096	Approved
0.6271	Remote Similarity	NPD5343	Approved
0.6226	Remote Similarity	NPD9115	Approved
0.6087	Remote Similarity	NPD5325	Clinical (unspecified phase)
0.6049	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.5932	Remote Similarity	NPD39	Approved
0.5932	Remote Similarity	NPD3174	Discontinued
0.5802	Remote Similarity	NPD5209	Approved
0.5667	Remote Similarity	NPD4222	Approved
0.5652	Remote Similarity	NPD4246	Clinical (unspecified phase)
0.5645	Remote Similarity	NPD3173	Approved
0.561	Remote Similarity	NPD4752	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