NPASS Compound

Structure

NPC474699 OpenBabel07101719242D 20 24 0 0 1 0 0 0 0 0999 V2000 2.2673 -4.2653 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0104 -3.5962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4158 -2.9563 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2673 -2.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0685 -2.5827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4013 -1.8090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6581 -2.4781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9945 -0.8955 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0649 -3.3917 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6092 -1.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.0594 -3.2872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2079 -1.9781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.2024 -2.0827 0.0000 C 0 0 2 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 1.4945 -0.0294 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5649 -4.2577 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5873 -0.9612 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2024 -3.0827 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 12 1 0 0 0 0 2 12 1 0 0 0 0 3 13 1 0 0 0 0 4 12 1 0 0 0 0 5 19 1 0 0 0 0 6 4 1 1 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 7 9 1 0 0 0 0 7 13 1 1 0 0 0 8 15 1 1 0 0 0 8 16 1 0 0 0 0 9 12 1 0 0 0 0 9 17 1 6 0 0 0 10 11 1 0 0 0 0 10 14 1 0 0 0 0 10 18 2 0 0 0 0 11 15 1 6 0 0 0 11 20 1 0 0 0 0 13 14 1 6 0 0 0 14 5 1 6 0 0 0 14 19 1 0 0 0 0 15 13 1 1 0 0 0 15 20 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	280.13
Volume:	266.529
LogP:	1.531
LogD:	1.708
LogS:	-3.82
# Rotatable Bonds:	0
TPSA:	82.59
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.605
Synthetic Accessibility Score:	6.192
Fsp3:	0.933
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.188
MDCK Permeability:	1.894565866678022e-05
Pgp-inhibitor:	0.002
Pgp-substrate:	0.891
Human Intestinal Absorption (HIA):	0.011
20% Bioavailability (F20%):	0.012
30% Bioavailability (F30%):	0.021

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.696
Plasma Protein Binding (PPB):	43.853416442871094%
Volume Distribution (VD):	1.134
Pgp-substrate:	64.91978454589844%

ADMET: Metabolism

CYP1A2-inhibitor:	0.013
CYP1A2-substrate:	0.871
CYP2C19-inhibitor:	0.015
CYP2C19-substrate:	0.828
CYP2C9-inhibitor:	0.006
CYP2C9-substrate:	0.048
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.159
CYP3A4-inhibitor:	0.009
CYP3A4-substrate:	0.251

ADMET: Excretion

Clearance (CL):	8.258
Half-life (T1/2):	0.683

ADMET: Toxicity

hERG Blockers:	0.029
Human Hepatotoxicity (H-HT):	0.125
Drug-inuced Liver Injury (DILI):	0.347
AMES Toxicity:	0.438
Rat Oral Acute Toxicity:	0.951
Maximum Recommended Daily Dose:	0.428
Skin Sensitization:	0.642
Carcinogencity:	0.839
Eye Corrosion:	0.38
Eye Irritation:	0.08
Respiratory Toxicity:	0.986

Download Data

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

Natural Product: NPC474699

Natural Product ID:	NPC474699
*Common Name:**	Coriolin
IUPAC Name:	n.a.
Synonyms:	Coriolin
Standard InCHIKey:	OMAFWWAJLVYWPU-ZOEJUPFXSA-N
Standard InCHI:	InChI=1S/C15H20O5/c1-12(2)4-6-7(9(12)17)13(3)14(5-19-14)10(18)11-15(13,20-11)8(6)16/h6-9,11,16-17H,4-5H2,1-3H3/t6-,7-,8-,9+,11+,13+,14-,15+/m0/s1
SMILES:	CC1(CC2C(C1O)C3(C4(CO4)C(=O)C5C3(C2O)O5)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL479523
PubChem CID:	10869683
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids

*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
NPO33	Coriolus consors	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Title]
NPO33	Coriolus consors	Species	Coriolaceae	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
MIC	3

Activity Type	# Activity
Organism	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	12.5	ug.mL-1	PMID[450022]
NPT3146	Organism	Micrococcus	Micrococcus	MIC	=	12.5	ug.mL-1	PMID[450022]
NPT1550	Organism	Bacillus anthracis	Bacillus anthracis	MIC	=	12.5	ug.mL-1	PMID[450022]

☑ 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 NPC474699 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	728
0.1-0.2	5566
0.2-0.3	14222
0.3-0.4	12070
0.4-0.5	7110
0.5-0.6	2605
0.6-0.7	335
0.7-0.8	60
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.8211	Intermediate Similarity	NPC470191
0.8	Intermediate Similarity	NPC475488
0.7802	Intermediate Similarity	NPC157328
0.7745	Intermediate Similarity	NPC114365
0.7745	Intermediate Similarity	NPC132304
0.7745	Intermediate Similarity	NPC154962
0.7745	Intermediate Similarity	NPC177518
0.7745	Intermediate Similarity	NPC123070
0.7745	Intermediate Similarity	NPC18433
0.7745	Intermediate Similarity	NPC18044
0.7745	Intermediate Similarity	NPC88890
0.7745	Intermediate Similarity	NPC169089
0.7692	Intermediate Similarity	NPC212340
0.7549	Intermediate Similarity	NPC292803
0.75	Intermediate Similarity	NPC168890
0.75	Intermediate Similarity	NPC278028
0.75	Intermediate Similarity	NPC328180
0.7431	Intermediate Similarity	NPC470115
0.7431	Intermediate Similarity	NPC470116
0.7407	Intermediate Similarity	NPC98870
0.7358	Intermediate Similarity	NPC278693
0.7358	Intermediate Similarity	NPC220773
0.7333	Intermediate Similarity	NPC214030
0.7333	Intermediate Similarity	NPC83108
0.73	Intermediate Similarity	NPC17336
0.7255	Intermediate Similarity	NPC476294
0.7255	Intermediate Similarity	NPC253995
0.7253	Intermediate Similarity	NPC470014
0.7228	Intermediate Similarity	NPC477264
0.7222	Intermediate Similarity	NPC182185
0.72	Intermediate Similarity	NPC217567
0.72	Intermediate Similarity	NPC76136
0.72	Intermediate Similarity	NPC329713
0.7196	Intermediate Similarity	NPC167044
0.7196	Intermediate Similarity	NPC329876
0.717	Intermediate Similarity	NPC474101
0.717	Intermediate Similarity	NPC44004
0.7158	Intermediate Similarity	NPC475689
0.713	Intermediate Similarity	NPC217041
0.7115	Intermediate Similarity	NPC259654
0.7115	Intermediate Similarity	NPC298266
0.7115	Intermediate Similarity	NPC471767
0.7103	Intermediate Similarity	NPC176756
0.7087	Intermediate Similarity	NPC211087
0.7087	Intermediate Similarity	NPC274695
0.708	Intermediate Similarity	NPC475401
0.7053	Intermediate Similarity	NPC473629
0.7048	Intermediate Similarity	NPC250594
0.7041	Intermediate Similarity	NPC226491
0.7041	Intermediate Similarity	NPC477614
0.7037	Intermediate Similarity	NPC117604
0.703	Intermediate Similarity	NPC298919
0.7018	Intermediate Similarity	NPC477092
0.701	Intermediate Similarity	NPC475729
0.701	Intermediate Similarity	NPC474215
0.7009	Intermediate Similarity	NPC41674
0.7009	Intermediate Similarity	NPC228311
0.7009	Intermediate Similarity	NPC469441
0.7	Intermediate Similarity	NPC469627
0.6991	Remote Similarity	NPC475305
0.697	Remote Similarity	NPC97032
0.6964	Remote Similarity	NPC300051
0.6952	Remote Similarity	NPC178853
0.6944	Remote Similarity	NPC469787
0.6944	Remote Similarity	NPC469788
0.6944	Remote Similarity	NPC290247
0.6944	Remote Similarity	NPC204884
0.6923	Remote Similarity	NPC179922
0.69	Remote Similarity	NPC65359
0.6881	Remote Similarity	NPC9013
0.6875	Remote Similarity	NPC97002
0.6875	Remote Similarity	NPC260852
0.6863	Remote Similarity	NPC470423
0.6863	Remote Similarity	NPC206878
0.6857	Remote Similarity	NPC471381
0.6847	Remote Similarity	NPC473062
0.6837	Remote Similarity	NPC474448
0.6832	Remote Similarity	NPC474065
0.6813	Remote Similarity	NPC477867
0.6813	Remote Similarity	NPC215030
0.6813	Remote Similarity	NPC125164
0.6804	Remote Similarity	NPC291310
0.6778	Remote Similarity	NPC96322
0.6774	Remote Similarity	NPC108014
0.6768	Remote Similarity	NPC31349
0.6765	Remote Similarity	NPC476189
0.6762	Remote Similarity	NPC109556
0.6762	Remote Similarity	NPC45125
0.6759	Remote Similarity	NPC473526
0.6759	Remote Similarity	NPC473701
0.6739	Remote Similarity	NPC68565
0.6739	Remote Similarity	NPC35871
0.6733	Remote Similarity	NPC246173
0.6731	Remote Similarity	NPC116683
0.6731	Remote Similarity	NPC476728
0.6729	Remote Similarity	NPC49393
0.6701	Remote Similarity	NPC292458
0.6701	Remote Similarity	NPC268578
0.6701	Remote Similarity	NPC217559
0.6701	Remote Similarity	NPC227170
0.6699	Remote Similarity	NPC470424
0.6698	Remote Similarity	NPC186861
0.6696	Remote Similarity	NPC475495
0.6667	Remote Similarity	NPC165069
0.6667	Remote Similarity	NPC470657
0.6667	Remote Similarity	NPC469350
0.6667	Remote Similarity	NPC476727
0.6667	Remote Similarity	NPC476726
0.6667	Remote Similarity	NPC471253
0.6667	Remote Similarity	NPC472745
0.6667	Remote Similarity	NPC59489
0.6667	Remote Similarity	NPC77089
0.6667	Remote Similarity	NPC139838
0.6667	Remote Similarity	NPC311904
0.6667	Remote Similarity	NPC254123
0.6637	Remote Similarity	NPC477093
0.6637	Remote Similarity	NPC475277
0.6637	Remote Similarity	NPC473522
0.6636	Remote Similarity	NPC477356
0.6635	Remote Similarity	NPC470031
0.6634	Remote Similarity	NPC61688
0.6632	Remote Similarity	NPC275243
0.6609	Remote Similarity	NPC475490
0.6606	Remote Similarity	NPC88469
0.6602	Remote Similarity	NPC228700
0.6602	Remote Similarity	NPC475788
0.6602	Remote Similarity	NPC472237
0.6602	Remote Similarity	NPC472238
0.66	Remote Similarity	NPC202937
0.6593	Remote Similarity	NPC311102
0.6574	Remote Similarity	NPC105725
0.6574	Remote Similarity	NPC470172
0.6566	Remote Similarity	NPC473350
0.6566	Remote Similarity	NPC51267
0.6562	Remote Similarity	NPC117137
0.6562	Remote Similarity	NPC66766
0.6556	Remote Similarity	NPC98711
0.6556	Remote Similarity	NPC475062
0.6552	Remote Similarity	NPC199937
0.6549	Remote Similarity	NPC472003
0.6545	Remote Similarity	NPC54737
0.6535	Remote Similarity	NPC191221
0.6535	Remote Similarity	NPC470009
0.6531	Remote Similarity	NPC472847
0.6531	Remote Similarity	NPC259173
0.6531	Remote Similarity	NPC69953
0.6526	Remote Similarity	NPC475725
0.6518	Remote Similarity	NPC227879
0.6518	Remote Similarity	NPC208333
0.6514	Remote Similarity	NPC107385
0.6514	Remote Similarity	NPC473406
0.6514	Remote Similarity	NPC123505
0.6509	Remote Similarity	NPC111187
0.6509	Remote Similarity	NPC471241
0.6509	Remote Similarity	NPC236176
0.6509	Remote Similarity	NPC190080
0.6509	Remote Similarity	NPC471150
0.65	Remote Similarity	NPC92139
0.65	Remote Similarity	NPC80700
0.65	Remote Similarity	NPC469626
0.65	Remote Similarity	NPC64862
0.65	Remote Similarity	NPC475491
0.65	Remote Similarity	NPC243746
0.6481	Remote Similarity	NPC478181
0.6481	Remote Similarity	NPC162024
0.6476	Remote Similarity	NPC287354
0.6476	Remote Similarity	NPC62407
0.6471	Remote Similarity	NPC200580
0.6465	Remote Similarity	NPC115995
0.6455	Remote Similarity	NPC327093
0.6455	Remote Similarity	NPC100078
0.6455	Remote Similarity	NPC470167
0.6449	Remote Similarity	NPC470188
0.6449	Remote Similarity	NPC477355
0.6444	Remote Similarity	NPC319007
0.6436	Remote Similarity	NPC263802
0.6429	Remote Similarity	NPC317066
0.6422	Remote Similarity	NPC471254
0.6422	Remote Similarity	NPC78127
0.6422	Remote Similarity	NPC471757
0.6422	Remote Similarity	NPC213528
0.6422	Remote Similarity	NPC244969
0.6422	Remote Similarity	NPC478176
0.6421	Remote Similarity	NPC70996
0.6421	Remote Similarity	NPC474003
0.6415	Remote Similarity	NPC142529
0.6415	Remote Similarity	NPC126156
0.6415	Remote Similarity	NPC91771
0.6413	Remote Similarity	NPC470243
0.641	Remote Similarity	NPC179429
0.6408	Remote Similarity	NPC477442
0.6408	Remote Similarity	NPC477433
0.6408	Remote Similarity	NPC476296
0.6408	Remote Similarity	NPC477444
0.64	Remote Similarity	NPC478111
0.6396	Remote Similarity	NPC314244
0.6396	Remote Similarity	NPC166079
0.6383	Remote Similarity	NPC228411
0.6381	Remote Similarity	NPC473331
0.6381	Remote Similarity	NPC477495

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 NPC474699 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	967
0.1-0.2	4740
0.2-0.3	2382
0.3-0.4	640
0.4-0.5	354
0.5-0.6	62
0.6-0.7	2
0.7-0.8	3
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
0.7745	Intermediate Similarity	NPD4056	Clinical (unspecified phase)
0.7745	Intermediate Similarity	NPD4057	Clinical (unspecified phase)
0.7624	Intermediate Similarity	NPD1700	Approved
0.625	Remote Similarity	NPD6059	Approved
0.625	Remote Similarity	NPD6319	Approved
0.625	Remote Similarity	NPD6054	Approved
0.621	Remote Similarity	NPD7078	Approved
0.6198	Remote Similarity	NPD6015	Approved
0.6198	Remote Similarity	NPD6016	Approved
0.6161	Remote Similarity	NPD8170	Clinical (unspecified phase)
0.6148	Remote Similarity	NPD5988	Approved
0.6148	Remote Similarity	NPD6370	Approved
0.6048	Remote Similarity	NPD7492	Approved
0.6034	Remote Similarity	NPD4634	Approved
0.602	Remote Similarity	NPD4802	Phase 2
0.602	Remote Similarity	NPD4238	Approved
0.6	Remote Similarity	NPD6616	Approved
0.5952	Remote Similarity	NPD8293	Discontinued
0.5926	Remote Similarity	NPD5282	Discontinued
0.5906	Remote Similarity	NPD7736	Approved
0.5897	Remote Similarity	NPD6371	Approved
0.5862	Remote Similarity	NPD7320	Approved
0.5862	Remote Similarity	NPD5345	Clinical (unspecified phase)
0.5784	Remote Similarity	NPD6435	Approved
0.5781	Remote Similarity	NPD6033	Approved
0.5776	Remote Similarity	NPD7899	Clinical (unspecified phase)
0.575	Remote Similarity	NPD4632	Approved
0.5714	Remote Similarity	NPD3703	Phase 2
0.5714	Remote Similarity	NPD3702	Approved
0.569	Remote Similarity	NPD5739	Approved
0.569	Remote Similarity	NPD6402	Approved
0.569	Remote Similarity	NPD7128	Approved
0.569	Remote Similarity	NPD6675	Approved
0.5684	Remote Similarity	NPD3698	Phase 2
0.5678	Remote Similarity	NPD6372	Approved
0.5678	Remote Similarity	NPD6373	Approved
0.5667	Remote Similarity	NPD8297	Approved
0.5641	Remote Similarity	NPD5697	Approved
0.5641	Remote Similarity	NPD5701	Approved
0.5625	Remote Similarity	NPD4244	Approved
0.5625	Remote Similarity	NPD4245	Approved
0.5625	Remote Similarity	NPD4789	Approved
0.5625	Remote Similarity	NPD4755	Approved
0.561	Remote Similarity	NPD6009	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