Structure

Physi-Chem Properties

Molecular Weight:  522.25
Volume:  520.496
LogP:  3.099
LogD:  2.428
LogS:  -3.528
# Rotatable Bonds:  7
TPSA:  128.89
# H-Bond Aceptor:  8
# H-Bond Donor:  2
# Rings:  4
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.285
Synthetic Accessibility Score:  4.923
Fsp3:  0.741
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.767
MDCK Permeability:  1.3101298463880084e-05
Pgp-inhibitor:  0.202
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.023
20% Bioavailability (F20%):  0.034
30% Bioavailability (F30%):  0.916

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.027
Plasma Protein Binding (PPB):  98.16320037841797%
Volume Distribution (VD):  0.278
Pgp-substrate:  0.9038491249084473%

ADMET: Metabolism

CYP1A2-inhibitor:  0.007
CYP1A2-substrate:  0.304
CYP2C19-inhibitor:  0.024
CYP2C19-substrate:  0.191
CYP2C9-inhibitor:  0.327
CYP2C9-substrate:  0.977
CYP2D6-inhibitor:  0.025
CYP2D6-substrate:  0.525
CYP3A4-inhibitor:  0.125
CYP3A4-substrate:  0.136

ADMET: Excretion

Clearance (CL):  1.294
Half-life (T1/2):  0.228

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.965
Drug-inuced Liver Injury (DILI):  0.521
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.225
Maximum Recommended Daily Dose:  0.967
Skin Sensitization:  0.571
Carcinogencity:  0.912
Eye Corrosion:  0.003
Eye Irritation:  0.014
Respiratory Toxicity:  0.94

Download Data

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

  Natural Product: NPC476926

Natural Product ID:  NPC476926
Common Name*:   sodium;[(E)-[(1R,4aR,4bS,8aS,10aS)-1-[2-[1-(carboxymethyl)-5-oxo-2H-pyrrol-4-yl]ethyl]-4b,8,8,10a-tetramethyl-1,3,4,4a,5,6,7,8a,9,10-decahydrophenanthren-2-ylidene]methyl] sulfate
IUPAC Name:   sodium;[(E)-[(1R,4aR,4bS,8aS,10aS)-1-[2-[1-(carboxymethyl)-5-oxo-2H-pyrrol-4-yl]ethyl]-4b,8,8,10a-tetramethyl-1,3,4,4a,5,6,7,8a,9,10-decahydrophenanthren-2-ylidene]methyl] sulfate
Synonyms:  
Standard InCHIKey:  ZZXFLLORLBZWOB-SSDJCRSCSA-M
Standard InCHI:  InChI=1S/C27H41NO7S.Na/c1-25(2)12-5-13-27(4)21(25)10-14-26(3)20(19(7-9-22(26)27)17-35-36(32,33)34)8-6-18-11-15-28(24(18)31)16-23(29)30;/h11,17,20-22H,5-10,12-16H2,1-4H3,(H,29,30)(H,32,33,34);/q;+1/p-1/b19-17+;/t20-,21-,22-,26+,27-;/m0./s1
SMILES:  C[C@]12CCCC([C@@H]1CC[C@]3([C@@H]2CC/C(=C\OS(=O)(=O)[O-])/[C@@H]3CCC4=CCN(C4=O)CC(=O)O)C)(C)C.[Na+]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   90683057
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001552] Sesterterpenoids
          • [CHEMONTID:0002881] Cheilanthane sesterterpenoids

*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
NPO33616 Coscinoderma sp. Species Spongiidae Eukaryota n.a. at a depth of 15 m off the coast of Weno Island, Chuuk state, Micronesia 2010-FEB PMID[24828374]
NPO33616 Coscinoderma sp. Species Spongiidae Eukaryota n.a. at a depth of 15 m off the coast of Weno Island, Chuuk state, Federated States of Micronesia 2010-FEB PMID[24828374]

☑ 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
NPT111 Cell Line K562 Homo sapiens LC50 = 1.3 ug/ml PMID[24828374]
NPT81 Cell Line A549 Homo sapiens LC50 = 1.4 ug/ml PMID[24828374]
NPT2 Others Unspecified MIC = 50 ug/ml PMID[24828374]
NPT2 Others Unspecified MIC = 62 ug/ml PMID[24828374]
NPT2 Others Unspecified IC50 > 100000 nM PMID[24828374]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 100 ug/ml PMID[24828374]
NPT3145 Organism Bacillus subtilis subsp. spizizenii ATCC 6633 Bacillus subtilis subsp. spizizenii ATCC 6633 MIC > 100 ug/ml PMID[24828374]
NPT3147 Organism Kocuria rhizophila Kocuria rhizophila MIC > 100 ug/ml PMID[24828374]
NPT1190 Organism Salmonella enterica Salmonella enterica MIC > 100 ug/ml PMID[24828374]
NPT2 Others Unspecified MIC > 100 ug/ml PMID[24828374]
NPT19 Organism Escherichia coli Escherichia coli MIC > 100 ug/ml PMID[24828374]

☑ 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 NPC476926 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
0.9798 High Similarity NPC476918
0.93 High Similarity NPC476921
0.8491 Intermediate Similarity NPC476920
0.835 Intermediate Similarity NPC477964
0.8148 Intermediate Similarity NPC476919
0.7925 Intermediate Similarity NPC476922
0.7636 Intermediate Similarity NPC476328
0.7573 Intermediate Similarity NPC17143
0.7573 Intermediate Similarity NPC47230
0.75 Intermediate Similarity NPC476276
0.7288 Intermediate Similarity NPC477121
0.7018 Intermediate Similarity NPC185929
0.7016 Intermediate Similarity NPC321197
0.6975 Remote Similarity NPC145501
0.6964 Remote Similarity NPC77703
0.6857 Remote Similarity NPC157479
0.6814 Remote Similarity NPC474001
0.6762 Remote Similarity NPC311769
0.6762 Remote Similarity NPC147513
0.6762 Remote Similarity NPC182106
0.6752 Remote Similarity NPC24596
0.675 Remote Similarity NPC469597
0.6723 Remote Similarity NPC474431
0.6723 Remote Similarity NPC474411
0.6639 Remote Similarity NPC63511
0.6639 Remote Similarity NPC469603
0.661 Remote Similarity NPC474099
0.6579 Remote Similarity NPC26597
0.6574 Remote Similarity NPC259252
0.6476 Remote Similarity NPC215474
0.646 Remote Similarity NPC325960
0.646 Remote Similarity NPC319692
0.646 Remote Similarity NPC247220
0.6429 Remote Similarity NPC476754
0.6423 Remote Similarity NPC176336
0.6422 Remote Similarity NPC324405
0.6417 Remote Similarity NPC218602
0.6404 Remote Similarity NPC184033
0.64 Remote Similarity NPC474006
0.6381 Remote Similarity NPC90150
0.6379 Remote Similarity NPC34193
0.6339 Remote Similarity NPC247316
0.6325 Remote Similarity NPC226509
0.6325 Remote Similarity NPC152718
0.6271 Remote Similarity NPC474827
0.6271 Remote Similarity NPC68001
0.6271 Remote Similarity NPC199831
0.6271 Remote Similarity NPC474828
0.6218 Remote Similarity NPC469958
0.6218 Remote Similarity NPC469604
0.6207 Remote Similarity NPC140685
0.6204 Remote Similarity NPC318515
0.6195 Remote Similarity NPC476753
0.6195 Remote Similarity NPC476752
0.6186 Remote Similarity NPC474244
0.6179 Remote Similarity NPC143173
0.6176 Remote Similarity NPC211641
0.6168 Remote Similarity NPC142683
0.6161 Remote Similarity NPC473056
0.6147 Remote Similarity NPC60350
0.6106 Remote Similarity NPC23217
0.6098 Remote Similarity NPC72688
0.6098 Remote Similarity NPC328052
0.6075 Remote Similarity NPC278459
0.6071 Remote Similarity NPC174342
0.6071 Remote Similarity NPC477973
0.6058 Remote Similarity NPC19907
0.6055 Remote Similarity NPC181743
0.6055 Remote Similarity NPC16287
0.6055 Remote Similarity NPC248758
0.6055 Remote Similarity NPC178025
0.6053 Remote Similarity NPC93027
0.605 Remote Similarity NPC58200
0.6033 Remote Similarity NPC230677
0.6033 Remote Similarity NPC233256
0.6033 Remote Similarity NPC195841
0.6019 Remote Similarity NPC472867
0.6019 Remote Similarity NPC219232
0.6019 Remote Similarity NPC469805
0.6019 Remote Similarity NPC128346
0.6019 Remote Similarity NPC469804
0.6019 Remote Similarity NPC472239
0.6019 Remote Similarity NPC200513
0.6 Remote Similarity NPC65661
0.6 Remote Similarity NPC470277
0.6 Remote Similarity NPC2709
0.5981 Remote Similarity NPC104545
0.5981 Remote Similarity NPC474509
0.5966 Remote Similarity NPC39473
0.5965 Remote Similarity NPC230064
0.5963 Remote Similarity NPC474976
0.5963 Remote Similarity NPC279639
0.5963 Remote Similarity NPC477124
0.5963 Remote Similarity NPC474790
0.5963 Remote Similarity NPC3856
0.595 Remote Similarity NPC119329
0.595 Remote Similarity NPC475239
0.5948 Remote Similarity NPC476174
0.5948 Remote Similarity NPC139459
0.5943 Remote Similarity NPC260385
0.5943 Remote Similarity NPC115515
0.5943 Remote Similarity NPC280654
0.5943 Remote Similarity NPC59436
0.5943 Remote Similarity NPC110094
0.5929 Remote Similarity NPC469546
0.5929 Remote Similarity NPC249312
0.5929 Remote Similarity NPC474844
0.5926 Remote Similarity NPC471898
0.5926 Remote Similarity NPC90055
0.5922 Remote Similarity NPC303613
0.5922 Remote Similarity NPC474228
0.592 Remote Similarity NPC44733
0.5913 Remote Similarity NPC151722
0.5913 Remote Similarity NPC474185
0.5909 Remote Similarity NPC19849
0.5909 Remote Similarity NPC96095
0.5909 Remote Similarity NPC477289
0.5909 Remote Similarity NPC472864
0.5909 Remote Similarity NPC25833
0.5897 Remote Similarity NPC9487
0.5897 Remote Similarity NPC471039
0.5897 Remote Similarity NPC29152
0.5893 Remote Similarity NPC43308
0.5893 Remote Similarity NPC476293
0.5893 Remote Similarity NPC75315
0.5893 Remote Similarity NPC163016
0.5888 Remote Similarity NPC199595
0.5887 Remote Similarity NPC470536
0.5882 Remote Similarity NPC251929
0.5882 Remote Similarity NPC265782
0.5882 Remote Similarity NPC2634
0.5877 Remote Similarity NPC101651
0.5877 Remote Similarity NPC159748
0.5872 Remote Similarity NPC469806
0.5872 Remote Similarity NPC320514
0.5872 Remote Similarity NPC3511
0.5872 Remote Similarity NPC142253
0.5872 Remote Similarity NPC94200
0.5872 Remote Similarity NPC469799
0.5865 Remote Similarity NPC20025
0.5865 Remote Similarity NPC474797
0.5865 Remote Similarity NPC474796
0.5865 Remote Similarity NPC329866
0.5862 Remote Similarity NPC471040
0.5862 Remote Similarity NPC477290
0.5862 Remote Similarity NPC324078
0.5856 Remote Similarity NPC8571
0.5856 Remote Similarity NPC474537
0.5856 Remote Similarity NPC34811
0.5856 Remote Similarity NPC189311
0.5856 Remote Similarity NPC474680
0.5856 Remote Similarity NPC106416
0.5856 Remote Similarity NPC29447
0.5856 Remote Similarity NPC86316
0.5856 Remote Similarity NPC76283
0.5849 Remote Similarity NPC471899
0.5849 Remote Similarity NPC472300
0.5849 Remote Similarity NPC471897
0.5849 Remote Similarity NPC107039
0.5847 Remote Similarity NPC156546
0.5847 Remote Similarity NPC52820
0.5841 Remote Similarity NPC472870
0.5841 Remote Similarity NPC472302
0.584 Remote Similarity NPC476290
0.5833 Remote Similarity NPC474348
0.5833 Remote Similarity NPC37038
0.5833 Remote Similarity NPC188785
0.5833 Remote Similarity NPC469797
0.5833 Remote Similarity NPC477057
0.5833 Remote Similarity NPC469798
0.5826 Remote Similarity NPC65120
0.5826 Remote Similarity NPC476187
0.5826 Remote Similarity NPC470113
0.5826 Remote Similarity NPC233455
0.5826 Remote Similarity NPC4036
0.5826 Remote Similarity NPC145067
0.5826 Remote Similarity NPC158030
0.5825 Remote Similarity NPC190035
0.5825 Remote Similarity NPC21944
0.5825 Remote Similarity NPC133253
0.5825 Remote Similarity NPC54123
0.582 Remote Similarity NPC470596
0.5818 Remote Similarity NPC97913
0.5818 Remote Similarity NPC200752
0.5818 Remote Similarity NPC21667
0.5818 Remote Similarity NPC307258
0.5818 Remote Similarity NPC118423
0.5818 Remote Similarity NPC105803
0.5818 Remote Similarity NPC215893
0.5818 Remote Similarity NPC167103
0.5812 Remote Similarity NPC150041
0.581 Remote Similarity NPC293803
0.581 Remote Similarity NPC65650
0.581 Remote Similarity NPC476346
0.581 Remote Similarity NPC255650
0.5806 Remote Similarity NPC470535
0.5804 Remote Similarity NPC195640
0.5804 Remote Similarity NPC186975
0.5804 Remote Similarity NPC322672
0.5804 Remote Similarity NPC324063

  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 NPC476926 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
0.646 Remote Similarity NPD5349 Clinical (unspecified phase)
0.6303 Remote Similarity NPD7333 Discontinued
0.625 Remote Similarity NPD6909 Approved
0.625 Remote Similarity NPD6908 Approved
0.6019 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5952 Remote Similarity NPD1376 Discontinued
0.5909 Remote Similarity NPD3668 Phase 3
0.5882 Remote Similarity NPD4691 Approved
0.5841 Remote Similarity NPD6672 Approved
0.5841 Remote Similarity NPD5737 Approved
0.5841 Remote Similarity NPD7513 Clinical (unspecified phase)
0.5826 Remote Similarity NPD7515 Phase 2
0.5804 Remote Similarity NPD7521 Approved
0.5804 Remote Similarity NPD7334 Approved
0.5804 Remote Similarity NPD7146 Approved
0.5804 Remote Similarity NPD6684 Approved
0.5804 Remote Similarity NPD6409 Approved
0.5804 Remote Similarity NPD5330 Approved
0.5784 Remote Similarity NPD4137 Phase 3
0.578 Remote Similarity NPD8028 Phase 2
0.5763 Remote Similarity NPD7732 Phase 3
0.5763 Remote Similarity NPD7614 Phase 1
0.5735 Remote Similarity NPD1482 Clinical (unspecified phase)
0.5728 Remote Similarity NPD4747 Approved
0.5726 Remote Similarity NPD7748 Approved
0.5714 Remote Similarity NPD4058 Approved
0.5702 Remote Similarity NPD6903 Approved
0.5676 Remote Similarity NPD3527 Clinical (unspecified phase)
0.5672 Remote Similarity NPD7122 Discontinued
0.5652 Remote Similarity NPD7285 Clinical (unspecified phase)
0.562 Remote Similarity NPD6404 Discontinued
0.5606 Remote Similarity NPD5991 Approved
0.5606 Remote Similarity NPD5990 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