Structure

Physi-Chem Properties

Molecular Weight:  228.14
Volume:  237.44
LogP:  0.394
LogD:  0.203
LogS:  -1.248
# Rotatable Bonds:  8
TPSA:  70.06
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.476
Synthetic Accessibility Score:  3.901
Fsp3:  0.75
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:  -4.45
MDCK Permeability:  2.850113196473103e-05
Pgp-inhibitor:  0.482
Pgp-substrate:  0.223
Human Intestinal Absorption (HIA):  0.646
20% Bioavailability (F20%):  0.196
30% Bioavailability (F30%):  0.239

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.976
Plasma Protein Binding (PPB):  66.8488540649414%
Volume Distribution (VD):  0.545
Pgp-substrate:  33.35359573364258%

ADMET: Metabolism

CYP1A2-inhibitor:  0.024
CYP1A2-substrate:  0.172
CYP2C19-inhibitor:  0.016
CYP2C19-substrate:  0.154
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.806
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.654
CYP3A4-inhibitor:  0.01
CYP3A4-substrate:  0.124

ADMET: Excretion

Clearance (CL):  6.138
Half-life (T1/2):  0.904

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.223
Drug-inuced Liver Injury (DILI):  0.069
AMES Toxicity:  0.103
Rat Oral Acute Toxicity:  0.494
Maximum Recommended Daily Dose:  0.105
Skin Sensitization:  0.425
Carcinogencity:  0.591
Eye Corrosion:  0.024
Eye Irritation:  0.675
Respiratory Toxicity:  0.233

Download Data

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

  Natural Product: NPC475221

Natural Product ID:  NPC475221
Common Name*:   (S,E)-9-Hydroxy-9-((Trans)-3-(Hydroxymethyl)Oxiran-2-Yl)Non-7-En-4-One
IUPAC Name:   (E,9S)-9-hydroxy-9-[(2S,3S)-3-(hydroxymethyl)oxiran-2-yl]non-7-en-4-one
Synonyms:  
Standard InCHIKey:  PQVKXVOYEJFIAJ-VRJDWZKZSA-N
Standard InCHI:  InChI=1S/C12H20O4/c1-2-5-9(14)6-3-4-7-10(15)12-11(8-13)16-12/h4,7,10-13,15H,2-3,5-6,8H2,1H3/b7-4+/t10-,11-,12-/m0/s1
SMILES:  CCCC(=O)CC/C=C/[C@@H]([C@@H]1O[C@H]1CO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL501334
PubChem CID:   44559141
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001334] Fatty alcohols

*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
NPO33429 menisporopsis theobromae bcc 3975 Species n.a. Eukaryota n.a. n.a. n.a. PMID[17067151]

☑ 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT91 Cell Line KB Homo sapiens IC50 > 30300.0 nM PMID[449990]
NPT639 Cell Line NCI-H187 Homo sapiens IC50 > 30300.0 nM PMID[449990]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 > 30300.0 nM PMID[449990]
NPT485 Organism Plasmodium falciparum (isolate K1 / Thailand) Plasmodium falciparum K1 IC50 > 30300.0 nM PMID[449990]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC > 303000.0 nM PMID[449990]

☑ 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 NPC475221 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.8333 Intermediate Similarity NPC25298
0.8254 Intermediate Similarity NPC258788
0.8088 Intermediate Similarity NPC130618
0.8028 Intermediate Similarity NPC473582
0.7887 Intermediate Similarity NPC474545
0.7887 Intermediate Similarity NPC326504
0.7887 Intermediate Similarity NPC473489
0.7826 Intermediate Similarity NPC475982
0.7761 Intermediate Similarity NPC19769
0.7746 Intermediate Similarity NPC470435
0.7703 Intermediate Similarity NPC318481
0.7692 Intermediate Similarity NPC321919
0.7692 Intermediate Similarity NPC81896
0.7647 Intermediate Similarity NPC83965
0.7576 Intermediate Similarity NPC113293
0.7536 Intermediate Similarity NPC478100
0.7536 Intermediate Similarity NPC478097
0.75 Intermediate Similarity NPC296436
0.75 Intermediate Similarity NPC476655
0.75 Intermediate Similarity NPC176215
0.75 Intermediate Similarity NPC478098
0.75 Intermediate Similarity NPC476654
0.75 Intermediate Similarity NPC476657
0.75 Intermediate Similarity NPC478099
0.7419 Intermediate Similarity NPC217188
0.7397 Intermediate Similarity NPC24590
0.7391 Intermediate Similarity NPC476659
0.7391 Intermediate Similarity NPC478101
0.7391 Intermediate Similarity NPC201356
0.7391 Intermediate Similarity NPC276299
0.7391 Intermediate Similarity NPC476656
0.7377 Intermediate Similarity NPC200772
0.7353 Intermediate Similarity NPC476658
0.7344 Intermediate Similarity NPC327388
0.7333 Intermediate Similarity NPC474278
0.7324 Intermediate Similarity NPC470436
0.7297 Intermediate Similarity NPC473948
0.7286 Intermediate Similarity NPC127091
0.7286 Intermediate Similarity NPC104537
0.7286 Intermediate Similarity NPC148192
0.7286 Intermediate Similarity NPC26500
0.7286 Intermediate Similarity NPC22101
0.7286 Intermediate Similarity NPC122627
0.7286 Intermediate Similarity NPC99619
0.7286 Intermediate Similarity NPC330426
0.7286 Intermediate Similarity NPC271921
0.7273 Intermediate Similarity NPC318306
0.7273 Intermediate Similarity NPC322186
0.7246 Intermediate Similarity NPC96414
0.7231 Intermediate Similarity NPC323498
0.7231 Intermediate Similarity NPC323436
0.7231 Intermediate Similarity NPC323597
0.7231 Intermediate Similarity NPC211752
0.72 Intermediate Similarity NPC49392
0.72 Intermediate Similarity NPC190400
0.7183 Intermediate Similarity NPC473559
0.7183 Intermediate Similarity NPC209327
0.7183 Intermediate Similarity NPC273508
0.7183 Intermediate Similarity NPC141481
0.7183 Intermediate Similarity NPC324981
0.7183 Intermediate Similarity NPC48218
0.7183 Intermediate Similarity NPC63873
0.7162 Intermediate Similarity NPC227814
0.7162 Intermediate Similarity NPC144995
0.7143 Intermediate Similarity NPC475210
0.7143 Intermediate Similarity NPC291260
0.7125 Intermediate Similarity NPC469809
0.7105 Intermediate Similarity NPC272267
0.7101 Intermediate Similarity NPC470808
0.7059 Intermediate Similarity NPC321838
0.7059 Intermediate Similarity NPC328776
0.7059 Intermediate Similarity NPC64971
0.7059 Intermediate Similarity NPC26810
0.7059 Intermediate Similarity NPC320305
0.7042 Intermediate Similarity NPC475443
0.7042 Intermediate Similarity NPC473829
0.7031 Intermediate Similarity NPC137538
0.7027 Intermediate Similarity NPC284006
0.7013 Intermediate Similarity NPC248775
0.7 Intermediate Similarity NPC470123
0.7 Intermediate Similarity NPC473722
0.6986 Remote Similarity NPC42526
0.6986 Remote Similarity NPC202011
0.6986 Remote Similarity NPC476660
0.6984 Remote Similarity NPC142092
0.6974 Remote Similarity NPC326661
0.6974 Remote Similarity NPC170148
0.697 Remote Similarity NPC474577
0.697 Remote Similarity NPC193975
0.6962 Remote Similarity NPC159714
0.6962 Remote Similarity NPC221510
0.6957 Remote Similarity NPC29697
0.6933 Remote Similarity NPC474321
0.6933 Remote Similarity NPC474280
0.6923 Remote Similarity NPC470148
0.6923 Remote Similarity NPC1180
0.6923 Remote Similarity NPC180725
0.6923 Remote Similarity NPC317899
0.6923 Remote Similarity NPC52264
0.6923 Remote Similarity NPC470149
0.6912 Remote Similarity NPC327112
0.6901 Remote Similarity NPC124586
0.6901 Remote Similarity NPC146811
0.6883 Remote Similarity NPC474026
0.6883 Remote Similarity NPC233071
0.6883 Remote Similarity NPC475711
0.6875 Remote Similarity NPC253364
0.6875 Remote Similarity NPC11383
0.6875 Remote Similarity NPC475046
0.6875 Remote Similarity NPC474252
0.6875 Remote Similarity NPC474959
0.6875 Remote Similarity NPC310450
0.6875 Remote Similarity NPC61177
0.6857 Remote Similarity NPC328089
0.6857 Remote Similarity NPC68343
0.6857 Remote Similarity NPC308457
0.6849 Remote Similarity NPC473772
0.6842 Remote Similarity NPC260396
0.6835 Remote Similarity NPC470147
0.6835 Remote Similarity NPC91332
0.6835 Remote Similarity NPC162741
0.6835 Remote Similarity NPC133226
0.6825 Remote Similarity NPC93639
0.6825 Remote Similarity NPC29234
0.6812 Remote Similarity NPC325929
0.6812 Remote Similarity NPC271282
0.6812 Remote Similarity NPC66460
0.68 Remote Similarity NPC325627
0.6795 Remote Similarity NPC13823
0.6795 Remote Similarity NPC68119
0.6795 Remote Similarity NPC473471
0.679 Remote Similarity NPC286770
0.679 Remote Similarity NPC284472
0.679 Remote Similarity NPC229799
0.6774 Remote Similarity NPC267110
0.6769 Remote Similarity NPC189677
0.6765 Remote Similarity NPC329249
0.6765 Remote Similarity NPC478095
0.6765 Remote Similarity NPC278202
0.6765 Remote Similarity NPC322002
0.6761 Remote Similarity NPC273600
0.6757 Remote Similarity NPC473361
0.6757 Remote Similarity NPC129630
0.6757 Remote Similarity NPC476037
0.6757 Remote Similarity NPC329904
0.6753 Remote Similarity NPC209113
0.6753 Remote Similarity NPC127118
0.6753 Remote Similarity NPC301207
0.6753 Remote Similarity NPC68819
0.6753 Remote Similarity NPC188860
0.675 Remote Similarity NPC474894
0.675 Remote Similarity NPC280367
0.6747 Remote Similarity NPC196381
0.6744 Remote Similarity NPC475441
0.6716 Remote Similarity NPC44542
0.6716 Remote Similarity NPC71755
0.6711 Remote Similarity NPC190859
0.6711 Remote Similarity NPC476590
0.6711 Remote Similarity NPC114727
0.6711 Remote Similarity NPC315843
0.6711 Remote Similarity NPC472174
0.6711 Remote Similarity NPC107654
0.6709 Remote Similarity NPC471537
0.6667 Remote Similarity NPC472072
0.6667 Remote Similarity NPC51809
0.6667 Remote Similarity NPC227135
0.6667 Remote Similarity NPC474818
0.6667 Remote Similarity NPC125365
0.6667 Remote Similarity NPC293114
0.6667 Remote Similarity NPC176329
0.6667 Remote Similarity NPC49302
0.6667 Remote Similarity NPC328311
0.6667 Remote Similarity NPC476703
0.6623 Remote Similarity NPC161038
0.6623 Remote Similarity NPC478196
0.6623 Remote Similarity NPC478191
0.6623 Remote Similarity NPC478194
0.6623 Remote Similarity NPC478192
0.6623 Remote Similarity NPC478193
0.6623 Remote Similarity NPC478195
0.6622 Remote Similarity NPC143396
0.6622 Remote Similarity NPC236208
0.662 Remote Similarity NPC25747
0.662 Remote Similarity NPC148233
0.662 Remote Similarity NPC294813
0.662 Remote Similarity NPC470320
0.662 Remote Similarity NPC13143
0.6618 Remote Similarity NPC478096
0.6615 Remote Similarity NPC284224
0.6615 Remote Similarity NPC474496
0.6588 Remote Similarity NPC287089
0.6585 Remote Similarity NPC161045
0.6585 Remote Similarity NPC44261
0.6582 Remote Similarity NPC221095
0.6582 Remote Similarity NPC182292
0.6582 Remote Similarity NPC279532
0.6582 Remote Similarity NPC133377
0.6582 Remote Similarity NPC279214
0.6579 Remote Similarity NPC132938
0.6579 Remote Similarity NPC329890

  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 NPC475221 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.7937 Intermediate Similarity NPD585 Clinical (unspecified phase)
0.6912 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6866 Remote Similarity NPD6109 Phase 1
0.6753 Remote Similarity NPD818 Approved
0.6753 Remote Similarity NPD819 Approved
0.6625 Remote Similarity NPD5790 Clinical (unspecified phase)
0.6575 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6437 Remote Similarity NPD7838 Discovery
0.6437 Remote Similarity NPD46 Approved
0.6437 Remote Similarity NPD6698 Approved
0.6389 Remote Similarity NPD3197 Phase 1
0.6375 Remote Similarity NPD4268 Approved
0.6375 Remote Similarity NPD4271 Approved
0.6364 Remote Similarity NPD7983 Approved
0.622 Remote Similarity NPD4820 Approved
0.622 Remote Similarity NPD4819 Approved
0.622 Remote Similarity NPD4821 Approved
0.622 Remote Similarity NPD4822 Approved
0.619 Remote Similarity NPD7154 Phase 3
0.6163 Remote Similarity NPD4249 Approved
0.6092 Remote Similarity NPD4251 Approved
0.6092 Remote Similarity NPD4250 Approved
0.6032 Remote Similarity NPD4265 Approved
0.6024 Remote Similarity NPD4252 Approved
0.6 Remote Similarity NPD6110 Phase 1
0.5976 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5915 Remote Similarity NPD9119 Approved
0.5915 Remote Similarity NPD69 Approved
0.589 Remote Similarity NPD368 Approved
0.5882 Remote Similarity NPD4269 Approved
0.5882 Remote Similarity NPD4270 Approved
0.5882 Remote Similarity NPD6435 Approved
0.5846 Remote Similarity NPD5343 Approved
0.5833 Remote Similarity NPD5344 Discontinued
0.5814 Remote Similarity NPD5362 Discontinued
0.5811 Remote Similarity NPD3210 Clinical (unspecified phase)
0.5795 Remote Similarity NPD5786 Approved
0.5781 Remote Similarity NPD4222 Approved
0.5781 Remote Similarity NPD39 Approved
0.5775 Remote Similarity NPD9118 Approved
0.5758 Remote Similarity NPD3173 Approved
0.5682 Remote Similarity NPD5363 Approved
0.5663 Remote Similarity NPD4756 Discovery
0.5658 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5652 Remote Similarity NPD3172 Approved
0.5652 Remote Similarity NPD7637 Suspended
0.5647 Remote Similarity NPD5368 Approved
0.5632 Remote Similarity NPD5332 Approved
0.5632 Remote Similarity NPD5331 Approved
0.5625 Remote Similarity NPD6096 Approved
0.5625 Remote Similarity NPD4225 Approved
0.5625 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5625 Remote Similarity NPD6097 Approved
0.5604 Remote Similarity NPD5370 Suspended

  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