Structure

Physi-Chem Properties

Molecular Weight:  232.15
Volume:  257.918
LogP:  4.311
LogD:  4.345
LogS:  -4.662
# Rotatable Bonds:  0
TPSA:  33.37
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.679
Synthetic Accessibility Score:  4.596
Fsp3:  0.467
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.654
MDCK Permeability:  2.3126758605940267e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.008
Human Intestinal Absorption (HIA):  0.019
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.426
Plasma Protein Binding (PPB):  99.25537872314453%
Volume Distribution (VD):  0.783
Pgp-substrate:  0.9640951752662659%

ADMET: Metabolism

CYP1A2-inhibitor:  0.33
CYP1A2-substrate:  0.686
CYP2C19-inhibitor:  0.077
CYP2C19-substrate:  0.814
CYP2C9-inhibitor:  0.208
CYP2C9-substrate:  0.919
CYP2D6-inhibitor:  0.057
CYP2D6-substrate:  0.866
CYP3A4-inhibitor:  0.234
CYP3A4-substrate:  0.249

ADMET: Excretion

Clearance (CL):  9.175
Half-life (T1/2):  0.486

ADMET: Toxicity

hERG Blockers:  0.012
Human Hepatotoxicity (H-HT):  0.937
Drug-inuced Liver Injury (DILI):  0.831
AMES Toxicity:  0.042
Rat Oral Acute Toxicity:  0.206
Maximum Recommended Daily Dose:  0.749
Skin Sensitization:  0.935
Carcinogencity:  0.865
Eye Corrosion:  0.013
Eye Irritation:  0.03
Respiratory Toxicity:  0.939

Download Data

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

  Natural Product: NPC286189

Natural Product ID:  NPC286189
Common Name*:   Glechomanolide
IUPAC Name:   (5E,9E,11aS)-3,6,10-trimethyl-7,8,11,11a-tetrahydro-4H-cyclodeca[b]furan-2-one
Synonyms:   Glechomanolide
Standard InCHIKey:  SLGKCOCDZZQQLY-HSLDFMSTSA-N
Standard InCHI:  InChI=1S/C15H20O2/c1-10-5-4-6-11(2)9-14-13(8-7-10)12(3)15(16)17-14/h6-7,14H,4-5,8-9H2,1-3H3/b10-7+,11-6+/t14-/m0/s1
SMILES:  C/C/1=CCC2=C(C)C(=O)O[C@H]2C/C(=C/CC1)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL450885
PubChem CID:   44593362
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones
          • [CHEMONTID:0001543] Sesquiterpene lactones
            • [CHEMONTID:0001771] Germacranolides and derivatives

*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
NPO29436 Vepris punctata Species Rutaceae Eukaryota wood Madagascar rainforest n.a. PMID[12713408]
NPO29436 Vepris punctata Species Rutaceae Eukaryota wood Madagascar Rainforest n.a. PMID[15165160]
NPO7929 Curcuma zedoaria Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[9868158]
NPO7929 Curcuma zedoaria Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7929 Curcuma zedoaria Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7929 Curcuma zedoaria Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7929 Curcuma zedoaria Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7929 Curcuma zedoaria Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29436 Vepris punctata Species Rutaceae 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT179 Cell Line A2780 Homo sapiens IC50 = 5.3 ug.mL-1 PMID[552763]

☑ 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 NPC286189 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
0.8548 High Similarity NPC182794
0.8525 High Similarity NPC44343
0.8525 High Similarity NPC210303
0.8525 High Similarity NPC179087
0.8413 Intermediate Similarity NPC248125
0.8361 Intermediate Similarity NPC151648
0.8276 Intermediate Similarity NPC478117
0.8154 Intermediate Similarity NPC474823
0.8036 Intermediate Similarity NPC236338
0.803 Intermediate Similarity NPC475004
0.8 Intermediate Similarity NPC225272
0.8 Intermediate Similarity NPC203335
0.7969 Intermediate Similarity NPC131174
0.7969 Intermediate Similarity NPC133904
0.7937 Intermediate Similarity NPC473737
0.7879 Intermediate Similarity NPC276290
0.7879 Intermediate Similarity NPC218477
0.7879 Intermediate Similarity NPC470256
0.7857 Intermediate Similarity NPC135698
0.7797 Intermediate Similarity NPC478120
0.7742 Intermediate Similarity NPC22897
0.7742 Intermediate Similarity NPC159650
0.7727 Intermediate Similarity NPC194871
0.7727 Intermediate Similarity NPC472266
0.7719 Intermediate Similarity NPC15789
0.7692 Intermediate Similarity NPC282760
0.7681 Intermediate Similarity NPC58956
0.7681 Intermediate Similarity NPC269206
0.7681 Intermediate Similarity NPC295633
0.7656 Intermediate Similarity NPC217940
0.7636 Intermediate Similarity NPC270706
0.7636 Intermediate Similarity NPC47946
0.7636 Intermediate Similarity NPC26600
0.7541 Intermediate Similarity NPC245002
0.7536 Intermediate Similarity NPC84038
0.7536 Intermediate Similarity NPC186531
0.75 Intermediate Similarity NPC197467
0.75 Intermediate Similarity NPC128280
0.746 Intermediate Similarity NPC133600
0.7429 Intermediate Similarity NPC474705
0.7429 Intermediate Similarity NPC222244
0.7429 Intermediate Similarity NPC16349
0.7424 Intermediate Similarity NPC470688
0.7424 Intermediate Similarity NPC470123
0.7391 Intermediate Similarity NPC469660
0.7385 Intermediate Similarity NPC68110
0.7385 Intermediate Similarity NPC474658
0.7361 Intermediate Similarity NPC123360
0.7361 Intermediate Similarity NPC68819
0.7361 Intermediate Similarity NPC235906
0.7344 Intermediate Similarity NPC79756
0.7344 Intermediate Similarity NPC19241
0.7344 Intermediate Similarity NPC26223
0.7324 Intermediate Similarity NPC15499
0.7324 Intermediate Similarity NPC476355
0.7324 Intermediate Similarity NPC117746
0.7324 Intermediate Similarity NPC474758
0.7324 Intermediate Similarity NPC294434
0.7324 Intermediate Similarity NPC259599
0.7313 Intermediate Similarity NPC37382
0.7313 Intermediate Similarity NPC191233
0.7297 Intermediate Similarity NPC270126
0.7286 Intermediate Similarity NPC129665
0.7286 Intermediate Similarity NPC163003
0.726 Intermediate Similarity NPC476028
0.726 Intermediate Similarity NPC471225
0.726 Intermediate Similarity NPC171204
0.726 Intermediate Similarity NPC141789
0.7246 Intermediate Similarity NPC88877
0.7246 Intermediate Similarity NPC151481
0.7246 Intermediate Similarity NPC476591
0.7222 Intermediate Similarity NPC329852
0.7222 Intermediate Similarity NPC155587
0.7222 Intermediate Similarity NPC329826
0.7222 Intermediate Similarity NPC469414
0.7213 Intermediate Similarity NPC159535
0.7213 Intermediate Similarity NPC151761
0.72 Intermediate Similarity NPC281132
0.7188 Intermediate Similarity NPC478095
0.7164 Intermediate Similarity NPC220766
0.7164 Intermediate Similarity NPC476589
0.7164 Intermediate Similarity NPC471556
0.7162 Intermediate Similarity NPC471465
0.7162 Intermediate Similarity NPC196653
0.7162 Intermediate Similarity NPC299235
0.7162 Intermediate Similarity NPC184737
0.7143 Intermediate Similarity NPC135863
0.7143 Intermediate Similarity NPC474193
0.7143 Intermediate Similarity NPC293437
0.7143 Intermediate Similarity NPC12283
0.7143 Intermediate Similarity NPC249850
0.7123 Intermediate Similarity NPC301207
0.7121 Intermediate Similarity NPC132243
0.7121 Intermediate Similarity NPC474774
0.7119 Intermediate Similarity NPC27264
0.7119 Intermediate Similarity NPC275316
0.7101 Intermediate Similarity NPC310210
0.7083 Intermediate Similarity NPC140287
0.7083 Intermediate Similarity NPC470686
0.7077 Intermediate Similarity NPC130953
0.7067 Intermediate Similarity NPC471299
0.7067 Intermediate Similarity NPC98557
0.7067 Intermediate Similarity NPC167881
0.7067 Intermediate Similarity NPC178277
0.7059 Intermediate Similarity NPC276299
0.7042 Intermediate Similarity NPC472254
0.7042 Intermediate Similarity NPC257618
0.7031 Intermediate Similarity NPC21946
0.7031 Intermediate Similarity NPC474084
0.7031 Intermediate Similarity NPC254095
0.7031 Intermediate Similarity NPC478096
0.7027 Intermediate Similarity NPC187568
0.7027 Intermediate Similarity NPC57744
0.7027 Intermediate Similarity NPC176329
0.7027 Intermediate Similarity NPC51809
0.7027 Intermediate Similarity NPC125365
0.7027 Intermediate Similarity NPC49302
0.7027 Intermediate Similarity NPC262747
0.7027 Intermediate Similarity NPC10572
0.7027 Intermediate Similarity NPC41780
0.7027 Intermediate Similarity NPC474818
0.7015 Intermediate Similarity NPC25747
0.7015 Intermediate Similarity NPC148233
0.7015 Intermediate Similarity NPC308457
0.7 Intermediate Similarity NPC470693
0.7 Intermediate Similarity NPC265574
0.7 Intermediate Similarity NPC148056
0.7 Intermediate Similarity NPC232812
0.6986 Remote Similarity NPC478192
0.6986 Remote Similarity NPC478191
0.6986 Remote Similarity NPC478194
0.6986 Remote Similarity NPC478196
0.6986 Remote Similarity NPC478195
0.6986 Remote Similarity NPC478193
0.6984 Remote Similarity NPC96663
0.697 Remote Similarity NPC15193
0.697 Remote Similarity NPC26810
0.6957 Remote Similarity NPC21998
0.6957 Remote Similarity NPC122627
0.6949 Remote Similarity NPC15912
0.6935 Remote Similarity NPC189677
0.6933 Remote Similarity NPC209135
0.6933 Remote Similarity NPC473471
0.6933 Remote Similarity NPC108816
0.6933 Remote Similarity NPC474816
0.6933 Remote Similarity NPC128276
0.6933 Remote Similarity NPC279214
0.6933 Remote Similarity NPC93763
0.6933 Remote Similarity NPC221095
0.6923 Remote Similarity NPC116543
0.6923 Remote Similarity NPC169575
0.6923 Remote Similarity NPC40746
0.6923 Remote Similarity NPC474267
0.6923 Remote Similarity NPC97570
0.6923 Remote Similarity NPC82465
0.6923 Remote Similarity NPC222852
0.6923 Remote Similarity NPC59097
0.6912 Remote Similarity NPC273600
0.6912 Remote Similarity NPC19769
0.6912 Remote Similarity NPC96414
0.6901 Remote Similarity NPC64234
0.6901 Remote Similarity NPC37929
0.6892 Remote Similarity NPC127118
0.6892 Remote Similarity NPC27205
0.6892 Remote Similarity NPC209113
0.6885 Remote Similarity NPC106531
0.6885 Remote Similarity NPC151919
0.6883 Remote Similarity NPC24417
0.6883 Remote Similarity NPC325031
0.6883 Remote Similarity NPC471325
0.6875 Remote Similarity NPC471279
0.6875 Remote Similarity NPC265551
0.6875 Remote Similarity NPC212730
0.6875 Remote Similarity NPC129150
0.6875 Remote Similarity NPC294938
0.6875 Remote Similarity NPC471277
0.6866 Remote Similarity NPC155849
0.6866 Remote Similarity NPC2328
0.6866 Remote Similarity NPC475073
0.6857 Remote Similarity NPC238223
0.6857 Remote Similarity NPC475760
0.6857 Remote Similarity NPC477117
0.6857 Remote Similarity NPC287705
0.6849 Remote Similarity NPC476590
0.6849 Remote Similarity NPC114727
0.6842 Remote Similarity NPC12907
0.6825 Remote Similarity NPC173157
0.6825 Remote Similarity NPC474913
0.6818 Remote Similarity NPC98519
0.6818 Remote Similarity NPC309408
0.6812 Remote Similarity NPC124586
0.6812 Remote Similarity NPC116013
0.6812 Remote Similarity NPC146811
0.6812 Remote Similarity NPC475555
0.6812 Remote Similarity NPC475675
0.6812 Remote Similarity NPC201356
0.6806 Remote Similarity NPC316185
0.68 Remote Similarity NPC474760
0.68 Remote Similarity NPC97516
0.68 Remote Similarity NPC116177

  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 NPC286189 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
0.7586 Intermediate Similarity NPD6927 Phase 3
0.7424 Intermediate Similarity NPD2685 Clinical (unspecified phase)
0.642 Remote Similarity NPD6400 Clinical (unspecified phase)
0.6375 Remote Similarity NPD5209 Approved
0.6341 Remote Similarity NPD1733 Clinical (unspecified phase)
0.6286 Remote Similarity NPD5325 Clinical (unspecified phase)
0.6271 Remote Similarity NPD6096 Approved
0.6271 Remote Similarity NPD6097 Approved
0.623 Remote Similarity NPD5343 Approved
0.6173 Remote Similarity NPD4752 Clinical (unspecified phase)
0.6129 Remote Similarity NPD4220 Pre-registration
0.6087 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6029 Remote Similarity NPD9119 Approved
0.6029 Remote Similarity NPD69 Approved
0.5952 Remote Similarity NPD1694 Approved
0.5897 Remote Similarity NPD1452 Discontinued
0.5897 Remote Similarity NPD8039 Approved
0.5882 Remote Similarity NPD9118 Approved
0.5797 Remote Similarity NPD6109 Phase 1
0.5795 Remote Similarity NPD6698 Approved
0.5795 Remote Similarity NPD7838 Discovery
0.5795 Remote Similarity NPD46 Approved
0.5765 Remote Similarity NPD6082 Clinical (unspecified phase)
0.575 Remote Similarity NPD4756 Discovery
0.5732 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5714 Remote Similarity NPD7154 Phase 3
0.5682 Remote Similarity NPD1695 Approved
0.5652 Remote Similarity NPD8779 Phase 3
0.5645 Remote Similarity NPD39 Approved
0.5645 Remote Similarity NPD3174 Discontinued
0.5632 Remote Similarity NPD1282 Approved
0.5618 Remote Similarity NPD5785 Approved
0.56 Remote Similarity NPD4247 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