NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	224.1
Volume:	232.167
LogP:	0.722
LogD:	1.093
LogS:	-2.32
# Rotatable Bonds:	2
TPSA:	74.6
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	1
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.717
Synthetic Accessibility Score:	4.182
Fsp3:	0.5
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:	-4.406
MDCK Permeability:	2.274499820487108e-05
Pgp-inhibitor:	0.073
Pgp-substrate:	0.004
Human Intestinal Absorption (HIA):	0.103
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.797
Plasma Protein Binding (PPB):	60.468536376953125%
Volume Distribution (VD):	0.306
Pgp-substrate:	33.12200164794922%

ADMET: Metabolism

CYP1A2-inhibitor:	0.02
CYP1A2-substrate:	0.242
CYP2C19-inhibitor:	0.036
CYP2C19-substrate:	0.619
CYP2C9-inhibitor:	0.025
CYP2C9-substrate:	0.93
CYP2D6-inhibitor:	0.005
CYP2D6-substrate:	0.23
CYP3A4-inhibitor:	0.01
CYP3A4-substrate:	0.266

ADMET: Excretion

Clearance (CL):	2.747
Half-life (T1/2):	0.695

ADMET: Toxicity

hERG Blockers:	0.035
Human Hepatotoxicity (H-HT):	0.475
Drug-inuced Liver Injury (DILI):	0.48
AMES Toxicity:	0.86
Rat Oral Acute Toxicity:	0.917
Maximum Recommended Daily Dose:	0.085
Skin Sensitization:	0.762
Carcinogencity:	0.902
Eye Corrosion:	0.021
Eye Irritation:	0.737
Respiratory Toxicity:	0.079

Download Data

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

Natural Product: NPC122244

Natural Product ID:	NPC122244
*Common Name:**	Acremine B
IUPAC Name:	(5R)-5-hydroxy-2-[(E)-3-hydroxy-3-methylbut-1-enyl]-5-methylcyclohex-2-ene-1,4-dione
Synonyms:
Standard InCHIKey:	YFSJQGDPFJQBQL-ZYOFXKKJSA-N
Standard InCHI:	InChI=1S/C12H16O4/c1-11(2,15)5-4-8-6-10(14)12(3,16)7-9(8)13/h4-6,15-16H,7H2,1-3H3/b5-4+/t12-/m1/s1
SMILES:	CC(C)(/C=C/C1=CC(=O)[C@@](C)(CC1=O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL254580
PubChem CID:	11356526
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001534] Quinone and hydroquinone lipids [CHEMONTID:0002802] Prenylquinones

*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
NPO32554	acremonium byssoides a20	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	PMID[18154270]

☑ 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	1
Others	1

Activity Type	# Activity
Cell Line	1
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT397	Cell Line	NCI-H460	Homo sapiens	IC50	=	36000.0	nM	PMID[553458]
NPT1095	Organism	Plasmopara viticola	Plasmopara viticola	Inhibition	=	57.7	%	PMID[553458]

☑ 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 NPC122244 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	165
0.1-0.2	1404
0.2-0.3	8131
0.3-0.4	17468
0.4-0.5	10723
0.5-0.6	3978
0.6-0.7	735
0.7-0.8	81
0.8-0.85	8
0.85-0.9	3
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.8533	High Similarity	NPC97173
0.8289	Intermediate Similarity	NPC82666
0.8182	Intermediate Similarity	NPC248624
0.8148	Intermediate Similarity	NPC187529
0.8	Intermediate Similarity	NPC190049
0.7949	Intermediate Similarity	NPC478122
0.7875	Intermediate Similarity	NPC275766
0.7857	Intermediate Similarity	NPC64985
0.7763	Intermediate Similarity	NPC12815
0.7763	Intermediate Similarity	NPC153660
0.7763	Intermediate Similarity	NPC238948
0.7763	Intermediate Similarity	NPC215745
0.76	Intermediate Similarity	NPC136473
0.76	Intermediate Similarity	NPC474060
0.7586	Intermediate Similarity	NPC32552
0.7564	Intermediate Similarity	NPC166018
0.7564	Intermediate Similarity	NPC225665
0.7564	Intermediate Similarity	NPC169056
0.75	Intermediate Similarity	NPC203819
0.747	Intermediate Similarity	NPC477784
0.747	Intermediate Similarity	NPC477785
0.747	Intermediate Similarity	NPC477786
0.7468	Intermediate Similarity	NPC4492
0.7468	Intermediate Similarity	NPC51391
0.7403	Intermediate Similarity	NPC106309
0.7397	Intermediate Similarity	NPC150162
0.7386	Intermediate Similarity	NPC142838
0.7294	Intermediate Similarity	NPC307112
0.7284	Intermediate Similarity	NPC231739
0.7273	Intermediate Similarity	NPC107848
0.7209	Intermediate Similarity	NPC196381
0.7195	Intermediate Similarity	NPC265980
0.7195	Intermediate Similarity	NPC63326
0.7183	Intermediate Similarity	NPC320421
0.7179	Intermediate Similarity	NPC84790
0.716	Intermediate Similarity	NPC473536
0.7159	Intermediate Similarity	NPC472676
0.7159	Intermediate Similarity	NPC472688
0.7128	Intermediate Similarity	NPC469851
0.7126	Intermediate Similarity	NPC103743
0.7126	Intermediate Similarity	NPC113370
0.7126	Intermediate Similarity	NPC476079
0.7108	Intermediate Similarity	NPC74086
0.7108	Intermediate Similarity	NPC160582
0.7105	Intermediate Similarity	NPC106613
0.7093	Intermediate Similarity	NPC15807
0.7093	Intermediate Similarity	NPC281172
0.7093	Intermediate Similarity	NPC70685
0.7089	Intermediate Similarity	NPC201562
0.7089	Intermediate Similarity	NPC29542
0.7089	Intermediate Similarity	NPC323437
0.7079	Intermediate Similarity	NPC131864
0.7073	Intermediate Similarity	NPC207772
0.7059	Intermediate Similarity	NPC16488
0.7059	Intermediate Similarity	NPC475083
0.7045	Intermediate Similarity	NPC72397
0.7037	Intermediate Similarity	NPC110725
0.7037	Intermediate Similarity	NPC7629
0.7037	Intermediate Similarity	NPC472305
0.7037	Intermediate Similarity	NPC151622
0.7033	Intermediate Similarity	NPC78159
0.7027	Intermediate Similarity	NPC53109
0.7027	Intermediate Similarity	NPC477830
0.7027	Intermediate Similarity	NPC143168
0.7024	Intermediate Similarity	NPC470298
0.7024	Intermediate Similarity	NPC474980
0.7011	Intermediate Similarity	NPC291712
0.7011	Intermediate Similarity	NPC315395
0.7011	Intermediate Similarity	NPC316426
0.7	Intermediate Similarity	NPC32944
0.7	Intermediate Similarity	NPC193396
0.6988	Remote Similarity	NPC27817
0.6979	Remote Similarity	NPC104161
0.6979	Remote Similarity	NPC469980
0.6979	Remote Similarity	NPC118902
0.6974	Remote Similarity	NPC472072
0.6974	Remote Similarity	NPC100719
0.6974	Remote Similarity	NPC166791
0.6974	Remote Similarity	NPC322035
0.6966	Remote Similarity	NPC36668
0.6966	Remote Similarity	NPC118011
0.6962	Remote Similarity	NPC288667
0.6951	Remote Similarity	NPC471061
0.6944	Remote Similarity	NPC281195
0.6941	Remote Similarity	NPC47450
0.6933	Remote Similarity	NPC7029
0.6932	Remote Similarity	NPC23622
0.6923	Remote Similarity	NPC262673
0.6897	Remote Similarity	NPC255174
0.6892	Remote Similarity	NPC269737
0.6889	Remote Similarity	NPC477684
0.6883	Remote Similarity	NPC278895
0.6883	Remote Similarity	NPC269985
0.6875	Remote Similarity	NPC186042
0.6875	Remote Similarity	NPC287878
0.6867	Remote Similarity	NPC169095
0.6854	Remote Similarity	NPC58271
0.6848	Remote Similarity	NPC181393
0.6848	Remote Similarity	NPC217624
0.6837	Remote Similarity	NPC469852
0.6835	Remote Similarity	NPC291062
0.6835	Remote Similarity	NPC94743
0.6829	Remote Similarity	NPC474197
0.6824	Remote Similarity	NPC474353
0.6818	Remote Similarity	NPC203795
0.6818	Remote Similarity	NPC472009
0.6813	Remote Similarity	NPC172101
0.6812	Remote Similarity	NPC137396
0.6809	Remote Similarity	NPC134083
0.6809	Remote Similarity	NPC471694
0.68	Remote Similarity	NPC322457
0.6795	Remote Similarity	NPC309466
0.679	Remote Similarity	NPC215050
0.6786	Remote Similarity	NPC19900
0.6782	Remote Similarity	NPC219966
0.6778	Remote Similarity	NPC95364
0.6778	Remote Similarity	NPC142159
0.6778	Remote Similarity	NPC474918
0.6774	Remote Similarity	NPC12727
0.6771	Remote Similarity	NPC224172
0.6768	Remote Similarity	NPC266514
0.6768	Remote Similarity	NPC469853
0.6753	Remote Similarity	NPC197089
0.6753	Remote Similarity	NPC142423
0.6753	Remote Similarity	NPC308294
0.675	Remote Similarity	NPC95863
0.675	Remote Similarity	NPC126061
0.6747	Remote Similarity	NPC257666
0.6747	Remote Similarity	NPC34110
0.6747	Remote Similarity	NPC266193
0.6744	Remote Similarity	NPC227925
0.6742	Remote Similarity	NPC472007
0.6739	Remote Similarity	NPC29798
0.6739	Remote Similarity	NPC282644
0.6714	Remote Similarity	NPC37644
0.6709	Remote Similarity	NPC469914
0.6706	Remote Similarity	NPC233352
0.6706	Remote Similarity	NPC138492
0.6706	Remote Similarity	NPC824
0.6705	Remote Similarity	NPC32037
0.6703	Remote Similarity	NPC224270
0.6667	Remote Similarity	NPC185253
0.6667	Remote Similarity	NPC58532
0.6667	Remote Similarity	NPC475994
0.6667	Remote Similarity	NPC215253
0.6667	Remote Similarity	NPC472677
0.6667	Remote Similarity	NPC325977
0.6667	Remote Similarity	NPC241507
0.6667	Remote Similarity	NPC258985
0.6667	Remote Similarity	NPC476627
0.6667	Remote Similarity	NPC275494
0.6667	Remote Similarity	NPC275098
0.6667	Remote Similarity	NPC243272
0.6667	Remote Similarity	NPC247586
0.6667	Remote Similarity	NPC7280
0.6667	Remote Similarity	NPC143210
0.6667	Remote Similarity	NPC229612
0.6667	Remote Similarity	NPC471409
0.6667	Remote Similarity	NPC472008
0.6667	Remote Similarity	NPC297398
0.6633	Remote Similarity	NPC131366
0.6633	Remote Similarity	NPC297281
0.6633	Remote Similarity	NPC473144
0.6632	Remote Similarity	NPC471916
0.663	Remote Similarity	NPC45579
0.663	Remote Similarity	NPC166110
0.6629	Remote Similarity	NPC261721
0.6629	Remote Similarity	NPC234038
0.6629	Remote Similarity	NPC194417
0.6628	Remote Similarity	NPC55869
0.6628	Remote Similarity	NPC67254
0.6628	Remote Similarity	NPC225515
0.6628	Remote Similarity	NPC171665
0.6627	Remote Similarity	NPC16279
0.6627	Remote Similarity	NPC186554
0.6627	Remote Similarity	NPC256640
0.6627	Remote Similarity	NPC1254
0.6627	Remote Similarity	NPC76966
0.6627	Remote Similarity	NPC205615
0.6623	Remote Similarity	NPC101670
0.6622	Remote Similarity	NPC86789
0.662	Remote Similarity	NPC474127
0.6596	Remote Similarity	NPC476245
0.6591	Remote Similarity	NPC469884
0.6588	Remote Similarity	NPC476624
0.6588	Remote Similarity	NPC113363
0.6588	Remote Similarity	NPC170394
0.6588	Remote Similarity	NPC472013
0.6585	Remote Similarity	NPC147438
0.6585	Remote Similarity	NPC264178
0.6585	Remote Similarity	NPC7382
0.6582	Remote Similarity	NPC263382
0.6582	Remote Similarity	NPC146376
0.6582	Remote Similarity	NPC125578
0.6582	Remote Similarity	NPC117804
0.6575	Remote Similarity	NPC283502
0.6575	Remote Similarity	NPC268185
0.6569	Remote Similarity	NPC89408
0.6562	Remote Similarity	NPC166770
0.6559	Remote Similarity	NPC248193

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 NPC122244 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	148
0.1-0.2	1786
0.2-0.3	4149
0.3-0.4	2302
0.4-0.5	594
0.5-0.6	151
0.6-0.7	16
0.7-0.8	4
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
0.716	Intermediate Similarity	NPD4756	Discovery
0.7108	Intermediate Similarity	NPD8259	Clinical (unspecified phase)
0.7093	Intermediate Similarity	NPD1696	Phase 3
0.7027	Intermediate Similarity	NPD2664	Clinical (unspecified phase)
0.6753	Remote Similarity	NPD7331	Phase 2
0.6512	Remote Similarity	NPD4695	Discontinued
0.6333	Remote Similarity	NPD5363	Approved
0.6329	Remote Similarity	NPD6108	Clinical (unspecified phase)
0.6264	Remote Similarity	NPD4519	Discontinued
0.6264	Remote Similarity	NPD4694	Approved
0.6264	Remote Similarity	NPD4623	Approved
0.6264	Remote Similarity	NPD5280	Approved
0.6264	Remote Similarity	NPD5690	Phase 2
0.6234	Remote Similarity	NPD4193	Approved
0.6234	Remote Similarity	NPD4192	Approved
0.6234	Remote Similarity	NPD4191	Approved
0.6234	Remote Similarity	NPD4194	Approved
0.6203	Remote Similarity	NPD7341	Phase 2
0.618	Remote Similarity	NPD4800	Clinical (unspecified phase)
0.6136	Remote Similarity	NPD4252	Approved
0.6125	Remote Similarity	NPD3704	Approved
0.6111	Remote Similarity	NPD6110	Phase 1
0.6087	Remote Similarity	NPD3574	Clinical (unspecified phase)
0.6064	Remote Similarity	NPD7285	Clinical (unspecified phase)
0.6044	Remote Similarity	NPD4197	Approved
0.6042	Remote Similarity	NPD5778	Approved
0.6042	Remote Similarity	NPD5779	Approved
0.604	Remote Similarity	NPD5211	Phase 2
0.6026	Remote Similarity	NPD368	Approved
0.6	Remote Similarity	NPD5209	Approved
0.6	Remote Similarity	NPD4269	Approved
0.6	Remote Similarity	NPD5785	Approved
0.6	Remote Similarity	NPD4270	Approved
0.6	Remote Similarity	NPD4058	Approved
0.5979	Remote Similarity	NPD5282	Discontinued
0.5978	Remote Similarity	NPD5329	Approved
0.5957	Remote Similarity	NPD4518	Approved
0.5938	Remote Similarity	NPD5281	Approved
0.5938	Remote Similarity	NPD5284	Approved
0.5922	Remote Similarity	NPD5141	Approved
0.5921	Remote Similarity	NPD8779	Phase 3
0.5918	Remote Similarity	NPD5210	Approved
0.5918	Remote Similarity	NPD4629	Approved
0.5914	Remote Similarity	NPD5786	Approved
0.5914	Remote Similarity	NPD5279	Phase 3
0.5897	Remote Similarity	NPD4246	Clinical (unspecified phase)
0.5895	Remote Similarity	NPD4753	Phase 2
0.5867	Remote Similarity	NPD342	Phase 1
0.5859	Remote Similarity	NPD5221	Approved
0.5859	Remote Similarity	NPD5220	Clinical (unspecified phase)
0.5859	Remote Similarity	NPD5222	Approved
0.5854	Remote Similarity	NPD4247	Clinical (unspecified phase)
0.5844	Remote Similarity	NPD287	Approved
0.5842	Remote Similarity	NPD5286	Approved
0.5842	Remote Similarity	NPD4696	Approved
0.5842	Remote Similarity	NPD5285	Approved
0.5824	Remote Similarity	NPD4221	Approved
0.5824	Remote Similarity	NPD4223	Phase 3
0.5814	Remote Similarity	NPD4687	Approved
0.58	Remote Similarity	NPD5173	Approved
0.5784	Remote Similarity	NPD5223	Approved
0.5773	Remote Similarity	NPD7983	Approved
0.5773	Remote Similarity	NPD5694	Approved
0.5747	Remote Similarity	NPD8264	Approved
0.5743	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.5741	Remote Similarity	NPD7601	Clinical (unspecified phase)
0.573	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.573	Remote Similarity	NPD3617	Approved
0.5729	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.5729	Remote Similarity	NPD6101	Approved
0.5728	Remote Similarity	NPD5226	Approved
0.5728	Remote Similarity	NPD5224	Approved
0.5728	Remote Similarity	NPD5225	Approved
0.5728	Remote Similarity	NPD4633	Approved
0.5714	Remote Similarity	NPD5133	Approved
0.5714	Remote Similarity	NPD5369	Approved
0.57	Remote Similarity	NPD4697	Phase 3
0.57	Remote Similarity	NPD7839	Suspended
0.5698	Remote Similarity	NPD4732	Discontinued
0.5694	Remote Similarity	NPD4220	Pre-registration
0.5673	Remote Similarity	NPD5174	Approved
0.5673	Remote Similarity	NPD5175	Approved
0.567	Remote Similarity	NPD5692	Phase 3
0.5667	Remote Similarity	NPD4195	Approved
0.5652	Remote Similarity	NPD3667	Approved
0.5648	Remote Similarity	NPD4634	Approved
0.5647	Remote Similarity	NPD4691	Approved
0.5644	Remote Similarity	NPD4755	Approved
0.5632	Remote Similarity	NPD5733	Approved
0.5625	Remote Similarity	NPD7115	Discovery
0.5612	Remote Similarity	NPD6050	Approved
0.5612	Remote Similarity	NPD6079	Approved
0.5612	Remote Similarity	NPD7637	Suspended
0.5612	Remote Similarity	NPD6411	Approved
0.5612	Remote Similarity	NPD4810	Clinical (unspecified phase)
0.5604	Remote Similarity	NPD4820	Approved
0.5604	Remote Similarity	NPD4821	Approved
0.5604	Remote Similarity	NPD4819	Approved
0.5604	Remote Similarity	NPD4822	Approved
0.56	Remote Similarity	NPD1698	Clinical (unspecified phase)
0.56	Remote Similarity	NPD5695	Phase 3

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