Structure

Physi-Chem Properties

Molecular Weight:  198.09
Volume:  200.211
LogP:  0.903
LogD:  0.667
LogS:  -2.138
# Rotatable Bonds:  0
TPSA:  60.44
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.43
Synthetic Accessibility Score:  3.418
Fsp3:  0.7
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.516
MDCK Permeability:  6.255393236642703e-05
Pgp-inhibitor:  0.982
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.454

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.989
Plasma Protein Binding (PPB):  50.02395248413086%
Volume Distribution (VD):  0.269
Pgp-substrate:  62.63959503173828%

ADMET: Metabolism

CYP1A2-inhibitor:  0.075
CYP1A2-substrate:  0.093
CYP2C19-inhibitor:  0.093
CYP2C19-substrate:  0.107
CYP2C9-inhibitor:  0.032
CYP2C9-substrate:  0.279
CYP2D6-inhibitor:  0.02
CYP2D6-substrate:  0.152
CYP3A4-inhibitor:  0.038
CYP3A4-substrate:  0.232

ADMET: Excretion

Clearance (CL):  9.795
Half-life (T1/2):  0.882

ADMET: Toxicity

hERG Blockers:  0.007
Human Hepatotoxicity (H-HT):  0.085
Drug-inuced Liver Injury (DILI):  0.619
AMES Toxicity:  0.881
Rat Oral Acute Toxicity:  0.023
Maximum Recommended Daily Dose:  0.36
Skin Sensitization:  0.925
Carcinogencity:  0.262
Eye Corrosion:  0.95
Eye Irritation:  0.81
Respiratory Toxicity:  0.142

Download Data

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

  Natural Product: NPC63873

Natural Product ID:  NPC63873
Common Name*:   7Alpha,8Alpha-Dihydroxy-3,5-Decadien-10-Olide
IUPAC Name:   (2R,4R,5S,6E,8Z)-4,5-dihydroxy-2-methyl-2,3,4,5-tetrahydrooxecin-10-one
Synonyms:  
Standard InCHIKey:  SAZJFRBQDIBJEF-RENNVBTOSA-N
Standard InCHI:  InChI=1S/C10H14O4/c1-7-6-9(12)8(11)4-2-3-5-10(13)14-7/h2-5,7-9,11-12H,6H2,1H3/b4-2+,5-3-/t7-,8+,9-/m1/s1
SMILES:  C[C@@H]1C[C@H]([C@H](/C=C/C=CC(=O)O1)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL455287
PubChem CID:   23631883
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001796] Oxocins

*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
NPO32626 Phomopsis sp. Species Valsaceae Eukaryota n.a. n.a. n.a. PMID[18336005]
NPO32626 Phomopsis sp. Species Valsaceae Eukaryota n.a. n.a. n.a. PMID[22233864]
NPO32626 Phomopsis sp. Species Valsaceae Eukaryota n.a. n.a. n.a. PMID[32686414]

☑ 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
NPT3660 Organism Fusarium avenaceum Fusarium avenaceum MIC > 500.0 ug.mL-1 PMID[515793]
NPT6148 Organism Helminthosporium maydis Helminthosporium maydis MIC = 500.0 ug.mL-1 PMID[515793]
NPT6149 Organism Penicillium islandicum Penicillium islandicum MIC > 500.0 ug.mL-1 PMID[515793]
NPT6150 Organism Ophiostoma minus Ophiostoma minus MIC > 500.0 ug.mL-1 PMID[515793]
NPT2781 Organism Fusarium moniliforme Gibberella moniliformis MIC > 500.0 ug.mL-1 PMID[515793]
NPT21 Organism Aspergillus niger Aspergillus niger MIC = 125.0 ug.mL-1 PMID[515793]
NPT635 Organism Botryotinia fuckeliana Botryotinia fuckeliana MIC = 500.0 ug.mL-1 PMID[515793]

☑ 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 NPC63873 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
0.8923 High Similarity NPC19769
0.8788 High Similarity NPC276299
0.8788 High Similarity NPC146811
0.873 High Similarity NPC97570
0.8507 High Similarity NPC201356
0.8485 Intermediate Similarity NPC470808
0.8462 Intermediate Similarity NPC26810
0.8451 Intermediate Similarity NPC315843
0.8358 Intermediate Similarity NPC96414
0.8358 Intermediate Similarity NPC470123
0.831 Intermediate Similarity NPC284006
0.8286 Intermediate Similarity NPC476037
0.8243 Intermediate Similarity NPC318481
0.8194 Intermediate Similarity NPC107654
0.8169 Intermediate Similarity NPC293114
0.8169 Intermediate Similarity NPC316185
0.8143 Intermediate Similarity NPC475982
0.8133 Intermediate Similarity NPC1180
0.8116 Intermediate Similarity NPC122627
0.8056 Intermediate Similarity NPC329890
0.8028 Intermediate Similarity NPC476012
0.7971 Intermediate Similarity NPC37382
0.7969 Intermediate Similarity NPC472808
0.7969 Intermediate Similarity NPC324224
0.7945 Intermediate Similarity NPC326504
0.7879 Intermediate Similarity NPC302564
0.7867 Intermediate Similarity NPC233071
0.7857 Intermediate Similarity NPC25298
0.7838 Intermediate Similarity NPC478195
0.7838 Intermediate Similarity NPC473582
0.7838 Intermediate Similarity NPC161038
0.7838 Intermediate Similarity NPC478194
0.7838 Intermediate Similarity NPC478191
0.7838 Intermediate Similarity NPC478196
0.7838 Intermediate Similarity NPC478192
0.7838 Intermediate Similarity NPC478193
0.7821 Intermediate Similarity NPC313677
0.7808 Intermediate Similarity NPC329914
0.7794 Intermediate Similarity NPC473737
0.7778 Intermediate Similarity NPC202011
0.7763 Intermediate Similarity NPC248775
0.7746 Intermediate Similarity NPC238223
0.7733 Intermediate Similarity NPC188860
0.7722 Intermediate Similarity NPC315559
0.7722 Intermediate Similarity NPC142111
0.7722 Intermediate Similarity NPC473315
0.7703 Intermediate Similarity NPC473489
0.7681 Intermediate Similarity NPC25747
0.7681 Intermediate Similarity NPC148233
0.7662 Intermediate Similarity NPC470148
0.7662 Intermediate Similarity NPC470149
0.7662 Intermediate Similarity NPC180725
0.7639 Intermediate Similarity NPC130618
0.7632 Intermediate Similarity NPC474026
0.7632 Intermediate Similarity NPC275530
0.7625 Intermediate Similarity NPC473308
0.7606 Intermediate Similarity NPC132286
0.7606 Intermediate Similarity NPC478097
0.76 Intermediate Similarity NPC260396
0.7595 Intermediate Similarity NPC251026
0.7571 Intermediate Similarity NPC478099
0.7571 Intermediate Similarity NPC282760
0.7571 Intermediate Similarity NPC478098
0.7571 Intermediate Similarity NPC273600
0.7568 Intermediate Similarity NPC470435
0.7564 Intermediate Similarity NPC470147
0.7564 Intermediate Similarity NPC133226
0.75 Intermediate Similarity NPC474823
0.75 Intermediate Similarity NPC26223
0.7467 Intermediate Similarity NPC474545
0.7465 Intermediate Similarity NPC124586
0.7439 Intermediate Similarity NPC208473
0.7429 Intermediate Similarity NPC308457
0.7403 Intermediate Similarity NPC475711
0.7397 Intermediate Similarity NPC475004
0.7391 Intermediate Similarity NPC113293
0.7361 Intermediate Similarity NPC478100
0.7353 Intermediate Similarity NPC322186
0.7353 Intermediate Similarity NPC222852
0.7353 Intermediate Similarity NPC318306
0.7333 Intermediate Similarity NPC185186
0.7333 Intermediate Similarity NPC327383
0.7308 Intermediate Similarity NPC182292
0.7297 Intermediate Similarity NPC329904
0.7297 Intermediate Similarity NPC473361
0.7273 Intermediate Similarity NPC68819
0.7273 Intermediate Similarity NPC326661
0.7273 Intermediate Similarity NPC470705
0.7262 Intermediate Similarity NPC470137
0.726 Intermediate Similarity NPC475760
0.725 Intermediate Similarity NPC315731
0.7237 Intermediate Similarity NPC114727
0.7237 Intermediate Similarity NPC474280
0.7237 Intermediate Similarity NPC476590
0.7222 Intermediate Similarity NPC478101
0.7206 Intermediate Similarity NPC223679
0.7195 Intermediate Similarity NPC161670
0.7183 Intermediate Similarity NPC475221
0.7162 Intermediate Similarity NPC151481
0.7162 Intermediate Similarity NPC470436
0.716 Intermediate Similarity NPC475046
0.716 Intermediate Similarity NPC310450
0.716 Intermediate Similarity NPC11383
0.716 Intermediate Similarity NPC474959
0.7143 Intermediate Similarity NPC473948
0.7143 Intermediate Similarity NPC285840
0.7143 Intermediate Similarity NPC327041
0.7143 Intermediate Similarity NPC55376
0.7101 Intermediate Similarity NPC159650
0.7101 Intermediate Similarity NPC22897
0.7089 Intermediate Similarity NPC473471
0.7089 Intermediate Similarity NPC279532
0.7089 Intermediate Similarity NPC28049
0.7083 Intermediate Similarity NPC476657
0.7083 Intermediate Similarity NPC476654
0.7083 Intermediate Similarity NPC476655
0.7073 Intermediate Similarity NPC229799
0.7073 Intermediate Similarity NPC286770
0.7073 Intermediate Similarity NPC44261
0.7073 Intermediate Similarity NPC284472
0.7067 Intermediate Similarity NPC59558
0.7059 Intermediate Similarity NPC129150
0.7059 Intermediate Similarity NPC472445
0.7059 Intermediate Similarity NPC135863
0.7059 Intermediate Similarity NPC44542
0.7051 Intermediate Similarity NPC203277
0.7051 Intermediate Similarity NPC301207
0.7051 Intermediate Similarity NPC127118
0.7051 Intermediate Similarity NPC209113
0.7037 Intermediate Similarity NPC184208
0.7037 Intermediate Similarity NPC469469
0.7037 Intermediate Similarity NPC297440
0.7037 Intermediate Similarity NPC8538
0.7013 Intermediate Similarity NPC470686
0.7013 Intermediate Similarity NPC474321
0.7 Intermediate Similarity NPC81896
0.7 Intermediate Similarity NPC98519
0.7 Intermediate Similarity NPC321919
0.7 Intermediate Similarity NPC130953
0.6988 Remote Similarity NPC475035
0.6986 Remote Similarity NPC476656
0.6986 Remote Similarity NPC475675
0.6986 Remote Similarity NPC476659
0.6986 Remote Similarity NPC475555
0.6974 Remote Similarity NPC475762
0.6962 Remote Similarity NPC49302
0.6962 Remote Similarity NPC51809
0.6962 Remote Similarity NPC474278
0.6962 Remote Similarity NPC474818
0.6962 Remote Similarity NPC125365
0.6962 Remote Similarity NPC176329
0.6957 Remote Similarity NPC254095
0.6957 Remote Similarity NPC187770
0.6957 Remote Similarity NPC474084
0.6944 Remote Similarity NPC476658
0.6941 Remote Similarity NPC118077
0.6941 Remote Similarity NPC475186
0.6933 Remote Similarity NPC143396
0.6923 Remote Similarity NPC200772
0.6914 Remote Similarity NPC121374
0.6912 Remote Similarity NPC86948
0.6912 Remote Similarity NPC230296
0.6905 Remote Similarity NPC475034
0.6901 Remote Similarity NPC15193
0.6897 Remote Similarity NPC473311
0.6875 Remote Similarity NPC279214
0.6875 Remote Similarity NPC477314
0.6875 Remote Similarity NPC221095
0.6867 Remote Similarity NPC161045
0.6867 Remote Similarity NPC169575
0.6867 Remote Similarity NPC116543
0.6867 Remote Similarity NPC40746
0.6857 Remote Similarity NPC322002
0.6857 Remote Similarity NPC329249
0.6849 Remote Similarity NPC471565
0.6849 Remote Similarity NPC471566
0.6849 Remote Similarity NPC182794
0.6849 Remote Similarity NPC471556
0.6835 Remote Similarity NPC49392
0.6835 Remote Similarity NPC190400
0.6829 Remote Similarity NPC150502
0.6829 Remote Similarity NPC474894
0.6829 Remote Similarity NPC24417
0.6824 Remote Similarity NPC61527
0.6824 Remote Similarity NPC469910
0.6812 Remote Similarity NPC212730
0.6812 Remote Similarity NPC293437
0.6812 Remote Similarity NPC294938
0.6812 Remote Similarity NPC319423
0.6812 Remote Similarity NPC265551
0.6812 Remote Similarity NPC323436
0.6812 Remote Similarity NPC249850
0.6806 Remote Similarity NPC68110
0.6806 Remote Similarity NPC210303
0.6806 Remote Similarity NPC475073
0.6806 Remote Similarity NPC44343
0.6806 Remote Similarity NPC474774
0.6806 Remote Similarity NPC2328
0.6806 Remote Similarity NPC179087
0.6806 Remote Similarity NPC29697

  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 NPC63873 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
0.6957 Remote Similarity NPD9119 Approved
0.6957 Remote Similarity NPD585 Clinical (unspecified phase)
0.6957 Remote Similarity NPD69 Approved
0.6897 Remote Similarity NPD7838 Discovery
0.6812 Remote Similarity NPD9118 Approved
0.6761 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6667 Remote Similarity NPD4247 Clinical (unspecified phase)
0.625 Remote Similarity NPD6109 Phase 1
0.6211 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6207 Remote Similarity NPD6400 Clinical (unspecified phase)
0.6154 Remote Similarity NPD46 Approved
0.6154 Remote Similarity NPD6698 Approved
0.6119 Remote Similarity NPD4220 Pre-registration
0.6118 Remote Similarity NPD5790 Clinical (unspecified phase)
0.6087 Remote Similarity NPD7983 Approved
0.6082 Remote Similarity NPD5344 Discontinued
0.5979 Remote Similarity NPD6648 Approved
0.5974 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5952 Remote Similarity NPD4756 Discovery
0.5882 Remote Similarity NPD4268 Approved
0.5882 Remote Similarity NPD4271 Approved
0.5876 Remote Similarity NPD4225 Approved
0.5844 Remote Similarity NPD3197 Phase 1
0.5806 Remote Similarity NPD5785 Approved
0.5795 Remote Similarity NPD5209 Approved
0.5747 Remote Similarity NPD4821 Approved
0.5747 Remote Similarity NPD4822 Approved
0.5747 Remote Similarity NPD4820 Approved
0.5747 Remote Similarity NPD4819 Approved
0.573 Remote Similarity NPD7154 Phase 3
0.5729 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5714 Remote Similarity NPD6927 Phase 3
0.5714 Remote Similarity NPD4249 Approved
0.5652 Remote Similarity NPD4251 Approved
0.5652 Remote Similarity NPD4250 Approved
0.5604 Remote Similarity NPD5363 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