Structure

Physi-Chem Properties

Molecular Weight:  816.23
Volume:  754.891
LogP:  0.374
LogD:  0.155
LogS:  -2.878
# Rotatable Bonds:  15
TPSA:  262.08
# H-Bond Aceptor:  17
# H-Bond Donor:  9
# Rings:  4
# Heavy Atoms:  19

MedChem Properties

QED Drug-Likeness Score:  0.069
Synthetic Accessibility Score:  6.13
Fsp3:  0.5
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.728
MDCK Permeability:  4.7521839405817445e-06
Pgp-inhibitor:  0.361
Pgp-substrate:  0.871
Human Intestinal Absorption (HIA):  0.616
20% Bioavailability (F20%):  0.408
30% Bioavailability (F30%):  0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.041
Plasma Protein Binding (PPB):  95.28107452392578%
Volume Distribution (VD):  0.408
Pgp-substrate:  7.721024513244629%

ADMET: Metabolism

CYP1A2-inhibitor:  0.063
CYP1A2-substrate:  0.014
CYP2C19-inhibitor:  0.088
CYP2C19-substrate:  0.053
CYP2C9-inhibitor:  0.047
CYP2C9-substrate:  0.548
CYP2D6-inhibitor:  0.033
CYP2D6-substrate:  0.222
CYP3A4-inhibitor:  0.428
CYP3A4-substrate:  0.062

ADMET: Excretion

Clearance (CL):  0.33
Half-life (T1/2):  0.344

ADMET: Toxicity

hERG Blockers:  0.085
Human Hepatotoxicity (H-HT):  0.564
Drug-inuced Liver Injury (DILI):  0.981
AMES Toxicity:  0.859
Rat Oral Acute Toxicity:  0.052
Maximum Recommended Daily Dose:  0.251
Skin Sensitization:  0.853
Carcinogencity:  0.793
Eye Corrosion:  0.003
Eye Irritation:  0.01
Respiratory Toxicity:  0.815

Download Data

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

  Natural Product: NPC475278

Natural Product ID:  NPC475278
Common Name*:   Aurantoside A
IUPAC Name:   2-[(2S,4Z)-4-[(2E,4E,6E,8E,10Z,12E)-11,13-dichloro-1-hydroxytetradeca-2,4,6,8,10,12-hexaenylidene]-1-[(2R,3R,4S,5R)-3-[(2S,3S,4S,5R)-3,4-dihydroxy-5-[(2S,3S,4R,5R)-4-hydroxy-3-methoxy-5-methyloxolan-2-yl]oxyoxan-2-yl]oxy-4,5-dihydroxyoxan-2-yl]-3,5-dioxopyrrolidin-2-yl]acetamide
Synonyms:  
Standard InCHIKey:  NLZFTTQPFPQXDX-JXYVBPDOSA-N
Standard InCHI:  InChI=1S/C36H46Cl2N2O15/c1-17(37)13-19(38)11-9-7-5-4-6-8-10-12-21(41)25-27(45)20(14-24(39)43)40(33(25)49)34-31(28(46)22(42)15-51-34)55-35-30(48)29(47)23(16-52-35)54-36-32(50-3)26(44)18(2)53-36/h4-13,18,20,22-23,26,28-32,34-36,41-42,44,46-48H,14-16H2,1-3H3,(H2,39,43)/b5-4+,8-6+,9-7+,12-10+,17-13+,19-11-,25-21-/t18-,20+,22-,23-,26-,28+,29-,30+,31-,32+,34-,35+,36+/m1/s1
SMILES:  CO[C@@H]1[C@H](O[C@@H]2CO[C@H]([C@H]([C@@H]2O)O)O[C@@H]2[C@@H](O)[C@H](O)CO[C@H]2N2C(=O)/C(=C(/C=C/C=C/C=C/C=C/C=C(/C=C(/Cl)C)Cl)O)/C(=O)[C@@H]2CC(=N)O)O[C@@H]([C@H]1O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL502660
PubChem CID:   54730003
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0000198] Oligosaccharides

*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
NPO25388 Siliquariaspongia japonica n.a. n.a. n.a. n.a. n.a. n.a. PMID[10425118]
NPO25388 Siliquariaspongia japonica n.a. n.a. n.a. 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
NPT168 Cell Line P388 Mus musculus IC50 > 5.0 ug.mL-1 PMID[464860]
NPT20 Organism Candida albicans Candida albicans IZ = 11.3 mm PMID[464860]
NPT20 Organism Candida albicans Candida albicans MIC = 1.25 ug.mL-1 PMID[464860]
NPT87 Organism Aspergillus fumigatus Aspergillus fumigatus IZ = 18.0 mm PMID[464860]
NPT87 Organism Aspergillus fumigatus Aspergillus fumigatus MIC = 0.16 ug.mL-1 PMID[464860]

☑ 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 NPC475278 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
1.0 High Similarity NPC247776
1.0 High Similarity NPC304299
1.0 High Similarity NPC309450
1.0 High Similarity NPC475266
0.9697 High Similarity NPC71866
0.8769 High Similarity NPC36254
0.8042 Intermediate Similarity NPC315848
0.8042 Intermediate Similarity NPC315210
0.6536 Remote Similarity NPC471256
0.6531 Remote Similarity NPC471255
0.6449 Remote Similarity NPC201128
0.6447 Remote Similarity NPC120335
0.6443 Remote Similarity NPC471263
0.6443 Remote Similarity NPC315058
0.6424 Remote Similarity NPC313962
0.6405 Remote Similarity NPC314361
0.6351 Remote Similarity NPC273185
0.6333 Remote Similarity NPC309525
0.6284 Remote Similarity NPC315188
0.6268 Remote Similarity NPC251122
0.6258 Remote Similarity NPC78189
0.625 Remote Similarity NPC316244
0.6242 Remote Similarity NPC471262
0.6242 Remote Similarity NPC230889
0.6214 Remote Similarity NPC475918
0.6205 Remote Similarity NPC315809
0.6205 Remote Similarity NPC314050
0.62 Remote Similarity NPC314629
0.619 Remote Similarity NPC477398
0.6159 Remote Similarity NPC314451
0.6159 Remote Similarity NPC313333
0.6159 Remote Similarity NPC313342
0.6159 Remote Similarity NPC314512
0.6104 Remote Similarity NPC316205
0.6104 Remote Similarity NPC315387
0.6103 Remote Similarity NPC8098
0.6103 Remote Similarity NPC197294
0.6103 Remote Similarity NPC45313
0.6103 Remote Similarity NPC183449
0.6096 Remote Similarity NPC103391
0.6096 Remote Similarity NPC472536
0.6084 Remote Similarity NPC298484
0.6071 Remote Similarity NPC55336
0.6069 Remote Similarity NPC314306
0.6067 Remote Similarity NPC477462
0.6065 Remote Similarity NPC477988
0.6053 Remote Similarity NPC470653
0.6053 Remote Similarity NPC470654
0.6053 Remote Similarity NPC470650
0.6036 Remote Similarity NPC475342
0.6023 Remote Similarity NPC327517
0.6023 Remote Similarity NPC319334
0.6023 Remote Similarity NPC322372
0.6013 Remote Similarity NPC99864
0.5987 Remote Similarity NPC325750
0.5974 Remote Similarity NPC314282
0.5973 Remote Similarity NPC235625
0.5959 Remote Similarity NPC314550
0.5959 Remote Similarity NPC469865
0.5956 Remote Similarity NPC256570
0.5956 Remote Similarity NPC158445
0.5956 Remote Similarity NPC156782
0.5956 Remote Similarity NPC70323
0.5956 Remote Similarity NPC157353
0.5956 Remote Similarity NPC54961
0.5956 Remote Similarity NPC23454
0.5956 Remote Similarity NPC262312
0.5956 Remote Similarity NPC282088
0.5956 Remote Similarity NPC192066
0.5956 Remote Similarity NPC17290
0.5956 Remote Similarity NPC35269
0.5956 Remote Similarity NPC3568
0.5949 Remote Similarity NPC120420
0.5948 Remote Similarity NPC97580
0.5948 Remote Similarity NPC469494
0.5948 Remote Similarity NPC204639
0.5944 Remote Similarity NPC315426
0.5935 Remote Similarity NPC329919
0.5935 Remote Similarity NPC477793
0.5935 Remote Similarity NPC470651
0.5935 Remote Similarity NPC470655
0.5929 Remote Similarity NPC188785
0.5924 Remote Similarity NPC316401
0.5906 Remote Similarity NPC6531
0.5903 Remote Similarity NPC474099
0.5894 Remote Similarity NPC470652
0.589 Remote Similarity NPC476875
0.5879 Remote Similarity NPC298067
0.5879 Remote Similarity NPC214821
0.5878 Remote Similarity NPC475975
0.5878 Remote Similarity NPC272166
0.5871 Remote Similarity NPC247902
0.5871 Remote Similarity NPC262880
0.5855 Remote Similarity NPC160688
0.5852 Remote Similarity NPC209047
0.5852 Remote Similarity NPC43074
0.5852 Remote Similarity NPC242503
0.5852 Remote Similarity NPC139782
0.5852 Remote Similarity NPC74672
0.585 Remote Similarity NPC478024
0.5845 Remote Similarity NPC476877
0.5844 Remote Similarity NPC469999
0.5839 Remote Similarity NPC30196
0.5838 Remote Similarity NPC297145
0.5838 Remote Similarity NPC321485
0.5838 Remote Similarity NPC197743
0.5838 Remote Similarity NPC317377
0.5833 Remote Similarity NPC471820
0.5833 Remote Similarity NPC471821
0.5818 Remote Similarity NPC193579
0.5818 Remote Similarity NPC298469
0.5809 Remote Similarity NPC111567
0.5809 Remote Similarity NPC473604
0.5809 Remote Similarity NPC475125
0.5809 Remote Similarity NPC475603
0.5809 Remote Similarity NPC61894
0.5809 Remote Similarity NPC309898
0.5809 Remote Similarity NPC186840
0.5809 Remote Similarity NPC263545
0.5809 Remote Similarity NPC473581
0.5809 Remote Similarity NPC282705
0.5809 Remote Similarity NPC182632
0.5809 Remote Similarity NPC473950
0.5809 Remote Similarity NPC15851
0.5808 Remote Similarity NPC61717
0.5808 Remote Similarity NPC244380
0.5806 Remote Similarity NPC477987
0.5806 Remote Similarity NPC329401
0.5801 Remote Similarity NPC471165
0.5799 Remote Similarity NPC2501
0.5793 Remote Similarity NPC207820
0.5793 Remote Similarity NPC475150
0.5789 Remote Similarity NPC122590
0.5789 Remote Similarity NPC473341
0.5783 Remote Similarity NPC52748
0.5782 Remote Similarity NPC181510
0.5782 Remote Similarity NPC47857
0.5782 Remote Similarity NPC168758
0.5779 Remote Similarity NPC293550
0.5779 Remote Similarity NPC16709
0.5779 Remote Similarity NPC477990
0.5779 Remote Similarity NPC50520
0.5779 Remote Similarity NPC323168
0.5779 Remote Similarity NPC477989
0.5779 Remote Similarity NPC111162
0.5779 Remote Similarity NPC315783
0.5775 Remote Similarity NPC474244
0.5769 Remote Similarity NPC473249
0.5767 Remote Similarity NPC180770
0.5764 Remote Similarity NPC476876
0.5762 Remote Similarity NPC17581
0.5762 Remote Similarity NPC476155
0.5759 Remote Similarity NPC41162
0.5753 Remote Similarity NPC473578
0.5752 Remote Similarity NPC469515
0.5745 Remote Similarity NPC233932
0.5743 Remote Similarity NPC60432
0.5743 Remote Similarity NPC1111
0.5743 Remote Similarity NPC261750
0.574 Remote Similarity NPC298005
0.574 Remote Similarity NPC36463
0.5733 Remote Similarity NPC66007
0.5733 Remote Similarity NPC296043
0.5732 Remote Similarity NPC173173
0.5724 Remote Similarity NPC313802
0.5724 Remote Similarity NPC67917
0.5724 Remote Similarity NPC314268
0.5724 Remote Similarity NPC477515
0.5723 Remote Similarity NPC69176
0.5723 Remote Similarity NPC139585
0.5723 Remote Similarity NPC284625
0.5705 Remote Similarity NPC313173
0.5698 Remote Similarity NPC475599
0.5698 Remote Similarity NPC113620
0.5698 Remote Similarity NPC100612
0.5698 Remote Similarity NPC187497
0.5698 Remote Similarity NPC174336
0.5697 Remote Similarity NPC162910
0.5695 Remote Similarity NPC329216
0.5695 Remote Similarity NPC65045
0.5694 Remote Similarity NPC74035
0.5686 Remote Similarity NPC11379
0.5683 Remote Similarity NPC469739
0.5679 Remote Similarity NPC472430
0.5679 Remote Similarity NPC82129
0.5677 Remote Similarity NPC316133
0.5677 Remote Similarity NPC318445
0.5676 Remote Similarity NPC29501
0.5671 Remote Similarity NPC302276
0.5667 Remote Similarity NPC471645
0.5664 Remote Similarity NPC475149
0.5664 Remote Similarity NPC471097
0.5663 Remote Similarity NPC470886
0.5658 Remote Similarity NPC106791
0.5658 Remote Similarity NPC470300
0.5658 Remote Similarity NPC201889
0.5655 Remote Similarity NPC472433
0.5641 Remote Similarity NPC477985
0.5641 Remote Similarity NPC471087
0.5641 Remote Similarity NPC326386

  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 NPC475278 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
0.6159 Remote Similarity NPD8342 Approved
0.6159 Remote Similarity NPD8341 Approved
0.6159 Remote Similarity NPD8340 Approved
0.6159 Remote Similarity NPD8299 Approved
0.6081 Remote Similarity NPD7641 Discontinued
0.6076 Remote Similarity NPD8387 Clinical (unspecified phase)
0.6069 Remote Similarity NPD6429 Approved
0.6069 Remote Similarity NPD6430 Approved
0.6065 Remote Similarity NPD8392 Approved
0.6065 Remote Similarity NPD8391 Approved
0.6065 Remote Similarity NPD8390 Approved
0.6013 Remote Similarity NPD8451 Approved
0.6013 Remote Similarity NPD8415 Approved
0.5974 Remote Similarity NPD8448 Approved
0.5921 Remote Similarity NPD6436 Phase 3
0.589 Remote Similarity NPD8384 Approved
0.5878 Remote Similarity NPD1000 Clinical (unspecified phase)
0.5852 Remote Similarity NPD8522 Clinical (unspecified phase)
0.5845 Remote Similarity NPD8045 Clinical (unspecified phase)
0.5845 Remote Similarity NPD1407 Approved
0.5817 Remote Similarity NPD7623 Phase 3
0.5817 Remote Similarity NPD7624 Clinical (unspecified phase)
0.58 Remote Similarity NPD6936 Clinical (unspecified phase)
0.58 Remote Similarity NPD6935 Phase 3
0.5779 Remote Similarity NPD7830 Approved
0.5779 Remote Similarity NPD7829 Approved
0.5769 Remote Similarity NPD7747 Phase 1
0.5769 Remote Similarity NPD7746 Phase 1
0.5733 Remote Similarity NPD4830 Approved
0.5733 Remote Similarity NPD4831 Approved
0.5733 Remote Similarity NPD4832 Approved
0.5714 Remote Similarity NPD8080 Discontinued
0.5705 Remote Similarity NPD8273 Phase 1
0.5695 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5686 Remote Similarity NPD7299 Clinical (unspecified phase)
0.5677 Remote Similarity NPD7642 Approved
0.5649 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5649 Remote Similarity NPD8444 Approved
0.5649 Remote Similarity NPD7739 Clinical (unspecified phase)
0.5643 Remote Similarity NPD6428 Approved
0.5632 Remote Similarity NPD8414 Discontinued
0.5608 Remote Similarity NPD6421 Discontinued
0.5605 Remote Similarity NPD4816 Clinical (unspecified phase)
0.56 Remote Similarity NPD8417 Discontinued
0.56 Remote Similarity NPD3731 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