Structure

Physi-Chem Properties

Molecular Weight:  292.2
Volume:  327.153
LogP:  4.653
LogD:  4.25
LogS:  -5.261
# Rotatable Bonds:  8
TPSA:  35.53
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.392
Synthetic Accessibility Score:  4.427
Fsp3:  0.611
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:  -4.53
MDCK Permeability:  2.5973544325097464e-05
Pgp-inhibitor:  0.888
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.248
30% Bioavailability (F30%):  0.952

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.056
Plasma Protein Binding (PPB):  97.46613311767578%
Volume Distribution (VD):  1.342
Pgp-substrate:  2.8948278427124023%

ADMET: Metabolism

CYP1A2-inhibitor:  0.934
CYP1A2-substrate:  0.773
CYP2C19-inhibitor:  0.925
CYP2C19-substrate:  0.876
CYP2C9-inhibitor:  0.874
CYP2C9-substrate:  0.043
CYP2D6-inhibitor:  0.922
CYP2D6-substrate:  0.066
CYP3A4-inhibitor:  0.955
CYP3A4-substrate:  0.528

ADMET: Excretion

Clearance (CL):  3.709
Half-life (T1/2):  0.338

ADMET: Toxicity

hERG Blockers:  0.007
Human Hepatotoxicity (H-HT):  0.886
Drug-inuced Liver Injury (DILI):  0.396
AMES Toxicity:  0.004
Rat Oral Acute Toxicity:  0.411
Maximum Recommended Daily Dose:  0.957
Skin Sensitization:  0.853
Carcinogencity:  0.09
Eye Corrosion:  0.016
Eye Irritation:  0.321
Respiratory Toxicity:  0.821

Download Data

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

  Natural Product: NPC220766

Natural Product ID:  NPC220766
Common Name*:   Spongosoritin A
IUPAC Name:   methyl (2Z)-2-[(5R)-3-ethyl-5-[(E,2R)-2-ethylhex-3-enyl]-5-methylfuran-2-ylidene]acetate
Synonyms:  
Standard InCHIKey:  AZOIPHHKXZQWIE-YREDLYEQSA-N
Standard InCHI:  InChI=1S/C18H28O3/c1-6-9-10-14(7-2)12-18(4)13-15(8-3)16(21-18)11-17(19)20-5/h9-11,13-14H,6-8,12H2,1-5H3/b10-9+,16-11-/t14-,18+/m0/s1
SMILES:  CC/C=C/[C@H](CC)C[C@]1(C)C=C(CC)/C(=C/C(=O)OC)/O1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL404390
PubChem CID:   11522149
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001983] Dihydrofurans

*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
NPO23381 Echinodorus macrophyllus Species Alismataceae Eukaryota n.a. n.a. n.a. PMID[10757722]
NPO23250 Plakortis angulospiculatus Species Plakinidae Eukaryota n.a. n.a. n.a. PMID[14703354]
NPO23250 Plakortis angulospiculatus Species Plakinidae Eukaryota n.a. n.a. n.a. PMID[1800643]
NPO23250 Plakortis angulospiculatus Species Plakinidae Eukaryota n.a. Brazil n.a. PMID[18177008]
NPO23250 Plakortis angulospiculatus Species Plakinidae Eukaryota n.a. caribbean n.a. PMID[20738102]
NPO19077 Nyssa sylvatica Species Nyssaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23250 Plakortis angulospiculatus Species Plakinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23381 Echinodorus macrophyllus Species Alismataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23121 Hedycarya angustifolia Species Monimiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6704 Aspergillus navahoensis Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19077 Nyssa sylvatica Species Nyssaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7363 Phaedranassa dubia Species Amaryllidaceae 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
NPT400 Cell Line MDA-MB-435 Homo sapiens IC50 > 25.0 ug.mL-1 PMID[514759]
NPT180 Cell Line HCT-8 Homo sapiens IC50 > 25.0 ug.mL-1 PMID[514759]
NPT399 Cell Line SF-295 Homo sapiens IC50 > 25.0 ug.mL-1 PMID[514759]
NPT116 Cell Line HL-60 Homo sapiens IC50 > 25.0 ug.mL-1 PMID[514759]
NPT1219 Organism Leishmania chagasi Leishmania chagasi IC50 = 2.5 ug.mL-1 PMID[514759]
NPT1219 Organism Leishmania chagasi Leishmania chagasi IC50 = 3.1 ug.mL-1 PMID[514759]
NPT27 Others Unspecified Activity = 1.8 % PMID[514759]
NPT27 Others Unspecified IC50 = 29.8 ug.mL-1 PMID[514759]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 > 10000.0 nM PMID[514759]
NPT2 Others Unspecified Selectivity index = 9.6 n.a. PMID[514759]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi IC50 = 25.7 ug.mL-1 PMID[514759]
NPT2 Others Unspecified Selectivity index = 1.15 n.a. PMID[514759]

☑ 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 NPC220766 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
0.9836 High Similarity NPC191233
0.9375 High Similarity NPC470693
0.9077 High Similarity NPC232812
0.8939 High Similarity NPC37929
0.8939 High Similarity NPC64234
0.8824 High Similarity NPC470686
0.8462 Intermediate Similarity NPC470688
0.8194 Intermediate Similarity NPC473825
0.7971 Intermediate Similarity NPC265574
0.7969 Intermediate Similarity NPC133600
0.7941 Intermediate Similarity NPC472266
0.7887 Intermediate Similarity NPC287878
0.7826 Intermediate Similarity NPC276290
0.7794 Intermediate Similarity NPC315115
0.7703 Intermediate Similarity NPC68156
0.7681 Intermediate Similarity NPC21998
0.7647 Intermediate Similarity NPC471566
0.7647 Intermediate Similarity NPC182794
0.7619 Intermediate Similarity NPC478117
0.7612 Intermediate Similarity NPC155849
0.7612 Intermediate Similarity NPC44343
0.7612 Intermediate Similarity NPC217940
0.7612 Intermediate Similarity NPC210303
0.7612 Intermediate Similarity NPC179087
0.7606 Intermediate Similarity NPC315285
0.7606 Intermediate Similarity NPC316029
0.7571 Intermediate Similarity NPC313444
0.7541 Intermediate Similarity NPC148056
0.7534 Intermediate Similarity NPC474758
0.75 Intermediate Similarity NPC271632
0.75 Intermediate Similarity NPC181587
0.75 Intermediate Similarity NPC15912
0.75 Intermediate Similarity NPC316185
0.75 Intermediate Similarity NPC291712
0.75 Intermediate Similarity NPC86948
0.7467 Intermediate Similarity NPC471225
0.7467 Intermediate Similarity NPC54996
0.7432 Intermediate Similarity NPC329852
0.7419 Intermediate Similarity NPC151919
0.7391 Intermediate Similarity NPC471556
0.7391 Intermediate Similarity NPC471565
0.7377 Intermediate Similarity NPC27264
0.7361 Intermediate Similarity NPC315597
0.7361 Intermediate Similarity NPC59558
0.7324 Intermediate Similarity NPC470256
0.7324 Intermediate Similarity NPC474823
0.7313 Intermediate Similarity NPC19241
0.7308 Intermediate Similarity NPC42470
0.7297 Intermediate Similarity NPC117746
0.7297 Intermediate Similarity NPC259599
0.7297 Intermediate Similarity NPC15499
0.7297 Intermediate Similarity NPC294434
0.7297 Intermediate Similarity NPC107654
0.7297 Intermediate Similarity NPC315843
0.7286 Intermediate Similarity NPC116013
0.7246 Intermediate Similarity NPC34883
0.7237 Intermediate Similarity NPC315394
0.7231 Intermediate Similarity NPC221763
0.7231 Intermediate Similarity NPC96663
0.7231 Intermediate Similarity NPC245002
0.7222 Intermediate Similarity NPC151481
0.7222 Intermediate Similarity NPC475004
0.7215 Intermediate Similarity NPC474028
0.7215 Intermediate Similarity NPC474439
0.7206 Intermediate Similarity NPC151648
0.7188 Intermediate Similarity NPC478120
0.7183 Intermediate Similarity NPC194871
0.7183 Intermediate Similarity NPC225272
0.7179 Intermediate Similarity NPC268827
0.7167 Intermediate Similarity NPC128280
0.7164 Intermediate Similarity NPC286189
0.7162 Intermediate Similarity NPC12815
0.7162 Intermediate Similarity NPC222244
0.7162 Intermediate Similarity NPC215745
0.7162 Intermediate Similarity NPC238948
0.7162 Intermediate Similarity NPC16349
0.716 Intermediate Similarity NPC281172
0.716 Intermediate Similarity NPC130030
0.7143 Intermediate Similarity NPC133904
0.7143 Intermediate Similarity NPC99182
0.7143 Intermediate Similarity NPC474005
0.7125 Intermediate Similarity NPC475714
0.7123 Intermediate Similarity NPC67183
0.7121 Intermediate Similarity NPC474825
0.7108 Intermediate Similarity NPC260343
0.7105 Intermediate Similarity NPC4509
0.7105 Intermediate Similarity NPC123360
0.7101 Intermediate Similarity NPC474658
0.7101 Intermediate Similarity NPC473737
0.7101 Intermediate Similarity NPC132243
0.7101 Intermediate Similarity NPC322457
0.7097 Intermediate Similarity NPC289388
0.7089 Intermediate Similarity NPC325031
0.7083 Intermediate Similarity NPC218477
0.7083 Intermediate Similarity NPC287705
0.7077 Intermediate Similarity NPC173157
0.7067 Intermediate Similarity NPC476355
0.7059 Intermediate Similarity NPC130953
0.7059 Intermediate Similarity NPC429928
0.7042 Intermediate Similarity NPC37382
0.7042 Intermediate Similarity NPC248125
0.7037 Intermediate Similarity NPC475706
0.7027 Intermediate Similarity NPC257618
0.7027 Intermediate Similarity NPC163003
0.7024 Intermediate Similarity NPC242877
0.7024 Intermediate Similarity NPC64913
0.7015 Intermediate Similarity NPC189700
0.7013 Intermediate Similarity NPC57744
0.7013 Intermediate Similarity NPC180290
0.7013 Intermediate Similarity NPC316324
0.7 Intermediate Similarity NPC270706
0.7 Intermediate Similarity NPC226066
0.7 Intermediate Similarity NPC16321
0.6986 Remote Similarity NPC473277
0.6986 Remote Similarity NPC476059
0.6986 Remote Similarity NPC476591
0.6986 Remote Similarity NPC269841
0.6986 Remote Similarity NPC473603
0.6986 Remote Similarity NPC88877
0.6984 Remote Similarity NPC244452
0.6977 Remote Similarity NPC282644
0.6977 Remote Similarity NPC29798
0.6974 Remote Similarity NPC469414
0.6974 Remote Similarity NPC68624
0.6974 Remote Similarity NPC329826
0.697 Remote Similarity NPC150717
0.6957 Remote Similarity NPC15193
0.6957 Remote Similarity NPC55376
0.6951 Remote Similarity NPC474424
0.6944 Remote Similarity NPC132286
0.6944 Remote Similarity NPC203335
0.6935 Remote Similarity NPC91765
0.6935 Remote Similarity NPC234084
0.6933 Remote Similarity NPC476489
0.6933 Remote Similarity NPC476490
0.6933 Remote Similarity NPC276336
0.6923 Remote Similarity NPC267231
0.6923 Remote Similarity NPC159535
0.6923 Remote Similarity NPC151761
0.6923 Remote Similarity NPC471220
0.6923 Remote Similarity NPC128276
0.6923 Remote Similarity NPC253749
0.6923 Remote Similarity NPC184737
0.6912 Remote Similarity NPC143810
0.6912 Remote Similarity NPC83838
0.6905 Remote Similarity NPC471956
0.6905 Remote Similarity NPC472302
0.6901 Remote Similarity NPC282760
0.6901 Remote Similarity NPC131174
0.6897 Remote Similarity NPC143210
0.6892 Remote Similarity NPC469660
0.6892 Remote Similarity NPC473361
0.6892 Remote Similarity NPC329904
0.6885 Remote Similarity NPC197467
0.6883 Remote Similarity NPC51391
0.6883 Remote Similarity NPC4492
0.6883 Remote Similarity NPC301525
0.6883 Remote Similarity NPC27205
0.6875 Remote Similarity NPC191643
0.6875 Remote Similarity NPC106531
0.6875 Remote Similarity NPC170167
0.686 Remote Similarity NPC175842
0.686 Remote Similarity NPC32944
0.686 Remote Similarity NPC193396
0.686 Remote Similarity NPC32494
0.686 Remote Similarity NPC166110
0.6857 Remote Similarity NPC68110
0.6849 Remote Similarity NPC238223
0.6849 Remote Similarity NPC310210
0.6842 Remote Similarity NPC140287
0.6835 Remote Similarity NPC178277
0.6835 Remote Similarity NPC264227
0.6835 Remote Similarity NPC472965
0.6835 Remote Similarity NPC471537
0.6835 Remote Similarity NPC63649
0.6829 Remote Similarity NPC196487
0.6829 Remote Similarity NPC14575
0.6825 Remote Similarity NPC236338
0.6824 Remote Similarity NPC142159
0.6824 Remote Similarity NPC95364
0.6818 Remote Similarity NPC12727
0.6818 Remote Similarity NPC474913
0.6812 Remote Similarity NPC26223
0.6812 Remote Similarity NPC98519
0.6812 Remote Similarity NPC309408
0.6812 Remote Similarity NPC127824
0.6812 Remote Similarity NPC79756
0.6806 Remote Similarity NPC146811
0.68 Remote Similarity NPC477084
0.6795 Remote Similarity NPC262747
0.6795 Remote Similarity NPC10572
0.6795 Remote Similarity NPC476439
0.679 Remote Similarity NPC471326
0.679 Remote Similarity NPC268122
0.679 Remote Similarity NPC221231
0.679 Remote Similarity NPC324170
0.679 Remote Similarity NPC94200
0.6786 Remote Similarity NPC125925
0.6782 Remote Similarity NPC59646
0.6782 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 NPC220766 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
0.7647 Intermediate Similarity NPD2685 Clinical (unspecified phase)
0.7 Intermediate Similarity NPD5325 Clinical (unspecified phase)
0.7 Intermediate Similarity NPD5209 Approved
0.6719 Remote Similarity NPD6927 Phase 3
0.6667 Remote Similarity NPD4220 Pre-registration
0.6538 Remote Similarity NPD8039 Approved
0.6479 Remote Similarity NPD4192 Approved
0.6479 Remote Similarity NPD4194 Approved
0.6479 Remote Similarity NPD4191 Approved
0.6479 Remote Similarity NPD4193 Approved
0.6386 Remote Similarity NPD4752 Clinical (unspecified phase)
0.6235 Remote Similarity NPD6400 Clinical (unspecified phase)
0.618 Remote Similarity NPD7838 Discovery
0.6118 Remote Similarity NPD7154 Phase 3
0.6023 Remote Similarity NPD1282 Approved
0.6 Remote Similarity NPD5343 Approved
0.5977 Remote Similarity NPD1694 Approved
0.5976 Remote Similarity NPD4756 Discovery
0.5895 Remote Similarity NPD8029 Clinical (unspecified phase)
0.589 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5833 Remote Similarity NPD6648 Approved
0.5795 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5795 Remote Similarity NPD1733 Clinical (unspecified phase)
0.5781 Remote Similarity NPD6096 Approved
0.5781 Remote Similarity NPD6097 Approved
0.5765 Remote Similarity NPD5790 Clinical (unspecified phase)
0.573 Remote Similarity NPD4249 Approved
0.5714 Remote Similarity NPD6051 Approved
0.5714 Remote Similarity NPD539 Approved
0.5694 Remote Similarity NPD8779 Phase 3
0.5692 Remote Similarity NPD3174 Discontinued
0.5667 Remote Similarity NPD4250 Approved
0.5667 Remote Similarity NPD4251 Approved
0.5652 Remote Similarity NPD46 Approved
0.5652 Remote Similarity NPD6698 Approved
0.5652 Remote Similarity NPD5207 Approved
0.5652 Remote Similarity NPD5785 Approved
0.5644 Remote Similarity NPD3134 Approved
0.5631 Remote Similarity NPD2067 Discontinued
0.56 Remote Similarity NPD5909 Discontinued

  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