Structure

Physi-Chem Properties

Molecular Weight:  572.24
Volume:  550.431
LogP:  0.999
LogD:  1.79
LogS:  -2.043
# Rotatable Bonds:  8
TPSA:  145.96
# H-Bond Aceptor:  9
# H-Bond Donor:  2
# Rings:  4
# Heavy Atoms:  11

MedChem Properties

QED Drug-Likeness Score:  0.25
Synthetic Accessibility Score:  5.012
Fsp3:  0.778
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:  -5.632
MDCK Permeability:  1.2103301742172334e-05
Pgp-inhibitor:  0.042
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.96
20% Bioavailability (F20%):  0.999
30% Bioavailability (F30%):  0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.014
Plasma Protein Binding (PPB):  97.45970916748047%
Volume Distribution (VD):  0.852
Pgp-substrate:  1.2871110439300537%

ADMET: Metabolism

CYP1A2-inhibitor:  0.004
CYP1A2-substrate:  0.637
CYP2C19-inhibitor:  0.023
CYP2C19-substrate:  0.557
CYP2C9-inhibitor:  0.279
CYP2C9-substrate:  0.948
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.321
CYP3A4-inhibitor:  0.092
CYP3A4-substrate:  0.124

ADMET: Excretion

Clearance (CL):  1.428
Half-life (T1/2):  0.048

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.945
Drug-inuced Liver Injury (DILI):  0.038
AMES Toxicity:  0.028
Rat Oral Acute Toxicity:  0.213
Maximum Recommended Daily Dose:  0.968
Skin Sensitization:  0.798
Carcinogencity:  0.933
Eye Corrosion:  0.003
Eye Irritation:  0.081
Respiratory Toxicity:  0.968

Download Data

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

  Natural Product: NPC476920

Natural Product ID:  NPC476920
Common Name*:   sodium;[(E)-[(1R,4aR,4bS,8aS,10aS)-4b,8,8,10a-tetramethyl-1-[2-[5-oxo-1-(2-sulfoethyl)-2H-pyrrol-4-yl]ethyl]-1,3,4,4a,5,6,7,8a,9,10-decahydrophenanthren-2-ylidene]methyl] sulfate
IUPAC Name:   sodium;[(E)-[(1R,4aR,4bS,8aS,10aS)-4b,8,8,10a-tetramethyl-1-[2-[5-oxo-1-(2-sulfoethyl)-2H-pyrrol-4-yl]ethyl]-1,3,4,4a,5,6,7,8a,9,10-decahydrophenanthren-2-ylidene]methyl] sulfate
Synonyms:  
Standard InCHIKey:  ADNUGGLWVBPHTQ-MNMNNRCESA-M
Standard InCHI:  InChI=1S/C27H43NO8S2.Na/c1-25(2)12-5-13-27(4)22(25)10-14-26(3)21(20(7-9-23(26)27)18-36-38(33,34)35)8-6-19-11-15-28(24(19)29)16-17-37(30,31)32;/h11,18,21-23H,5-10,12-17H2,1-4H3,(H,30,31,32)(H,33,34,35);/q;+1/p-1/b20-18+;/t21-,22-,23-,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)CCS(=O)(=O)O)C)(C)C.[Na+]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   90683093
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
NPT81 Cell Line A549 Homo sapiens LC50 = 2 ug/ml PMID[24828374]
NPT111 Cell Line K562 Homo sapiens LC50 = 4.6 ug/ml PMID[24828374]
NPT2 Others Unspecified MIC = 73 ug/ml PMID[24828374]
NPT2 Others Unspecified MIC = 90 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 NPC476920 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
0.9412 High Similarity NPC476919
0.9394 High Similarity NPC476922
0.8491 Intermediate Similarity NPC476926
0.8333 Intermediate Similarity NPC476918
0.819 Intermediate Similarity NPC477964
0.789 Intermediate Similarity NPC476921
0.7193 Intermediate Similarity NPC476328
0.7167 Intermediate Similarity NPC477121
0.7069 Intermediate Similarity NPC476276
0.7 Intermediate Similarity NPC176336
0.6842 Remote Similarity NPC77703
0.6729 Remote Similarity NPC157479
0.6636 Remote Similarity NPC182106
0.6636 Remote Similarity NPC311769
0.6636 Remote Similarity NPC147513
0.6455 Remote Similarity NPC259252
0.641 Remote Similarity NPC474001
0.6355 Remote Similarity NPC215474
0.6348 Remote Similarity NPC247220
0.6339 Remote Similarity NPC17143
0.6339 Remote Similarity NPC47230
0.6316 Remote Similarity NPC476754
0.6306 Remote Similarity NPC324405
0.6262 Remote Similarity NPC90150
0.626 Remote Similarity NPC72688
0.6228 Remote Similarity NPC247316
0.619 Remote Similarity NPC145501
0.6154 Remote Similarity NPC184033
0.6129 Remote Similarity NPC63511
0.6087 Remote Similarity NPC476753
0.6087 Remote Similarity NPC476752
0.6083 Remote Similarity NPC152718
0.6083 Remote Similarity NPC226509
0.608 Remote Similarity NPC143173
0.6058 Remote Similarity NPC211641
0.6053 Remote Similarity NPC473056
0.6047 Remote Similarity NPC474006
0.6015 Remote Similarity NPC321197
0.6 Remote Similarity NPC34193
0.6 Remote Similarity NPC328052
0.5984 Remote Similarity NPC469958
0.5968 Remote Similarity NPC24596
0.5948 Remote Similarity NPC478129
0.5948 Remote Similarity NPC93027
0.5935 Remote Similarity NPC185929
0.5932 Remote Similarity NPC325960
0.5932 Remote Similarity NPC319692
0.5905 Remote Similarity NPC219232
0.5905 Remote Similarity NPC128346
0.5872 Remote Similarity NPC474509
0.5859 Remote Similarity NPC469597
0.5833 Remote Similarity NPC115515
0.5833 Remote Similarity NPC140685
0.5827 Remote Similarity NPC474411
0.5827 Remote Similarity NPC44733
0.5827 Remote Similarity NPC474431
0.5826 Remote Similarity NPC249312
0.581 Remote Similarity NPC474228
0.581 Remote Similarity NPC303613
0.5806 Remote Similarity NPC230677
0.5804 Remote Similarity NPC25833
0.5789 Remote Similarity NPC43308
0.5772 Remote Similarity NPC474828
0.5772 Remote Similarity NPC68001
0.5772 Remote Similarity NPC474827
0.5772 Remote Similarity NPC199831
0.5769 Remote Similarity NPC265782
0.5769 Remote Similarity NPC2634
0.5769 Remote Similarity NPC251929
0.5755 Remote Similarity NPC329866
0.5755 Remote Similarity NPC474797
0.5755 Remote Similarity NPC474796
0.5752 Remote Similarity NPC76283
0.5714 Remote Similarity NPC190035
0.5714 Remote Similarity NPC307258
0.5714 Remote Similarity NPC21667
0.5714 Remote Similarity NPC54123
0.5701 Remote Similarity NPC293803
0.5701 Remote Similarity NPC255650
0.5691 Remote Similarity NPC476755
0.5691 Remote Similarity NPC58200
0.5678 Remote Similarity NPC475255
0.5673 Remote Similarity NPC139397
0.5669 Remote Similarity NPC218602
0.5667 Remote Similarity NPC80738
0.5664 Remote Similarity NPC318515
0.566 Remote Similarity NPC251705
0.5652 Remote Similarity NPC79698
0.5652 Remote Similarity NPC93778
0.5648 Remote Similarity NPC469796
0.5648 Remote Similarity NPC469793
0.5648 Remote Similarity NPC69408
0.5645 Remote Similarity NPC474563
0.5636 Remote Similarity NPC90965
0.5636 Remote Similarity NPC170793
0.5631 Remote Similarity NPC290350
0.5631 Remote Similarity NPC4370
0.5625 Remote Similarity NPC142683
0.5625 Remote Similarity NPC328351
0.5625 Remote Similarity NPC476290
0.5625 Remote Similarity NPC469603
0.5619 Remote Similarity NPC282593
0.5619 Remote Similarity NPC307176
0.5619 Remote Similarity NPC260040
0.5619 Remote Similarity NPC35734
0.5619 Remote Similarity NPC159577
0.5614 Remote Similarity NPC33881
0.5614 Remote Similarity NPC60350
0.5607 Remote Similarity NPC309852
0.5607 Remote Similarity NPC255021
0.5606 Remote Similarity NPC473573
0.56 Remote Similarity NPC475239

  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 NPC476920 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
0.6198 Remote Similarity NPD7333 Discontinued
0.5932 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5896 Remote Similarity NPD4478 Clinical (unspecified phase)
0.5804 Remote Similarity NPD3668 Phase 3
0.5769 Remote Similarity NPD4691 Approved
0.5676 Remote Similarity NPD8028 Phase 2
0.5673 Remote Similarity NPD4137 Phase 3
0.5619 Remote Similarity NPD4747 Approved
0.5607 Remote Similarity NPD4058 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