Structure

Physi-Chem Properties

Molecular Weight:  564.3
Volume:  572.383
LogP:  5.263
LogD:  3.1
LogS:  -3.601
# Rotatable Bonds:  8
TPSA:  128.89
# H-Bond Aceptor:  8
# H-Bond Donor:  2
# Rings:  4
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.211
Synthetic Accessibility Score:  5.144
Fsp3:  0.767
Lipinski Rule-of-5:  Rejected
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:  -5.644
MDCK Permeability:  1.0039031622000039e-05
Pgp-inhibitor:  0.125
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.136
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.987

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.071
Plasma Protein Binding (PPB):  98.24246978759766%
Volume Distribution (VD):  0.463
Pgp-substrate:  0.7661538124084473%

ADMET: Metabolism

CYP1A2-inhibitor:  0.009
CYP1A2-substrate:  0.406
CYP2C19-inhibitor:  0.046
CYP2C19-substrate:  0.777
CYP2C9-inhibitor:  0.347
CYP2C9-substrate:  0.964
CYP2D6-inhibitor:  0.018
CYP2D6-substrate:  0.45
CYP3A4-inhibitor:  0.268
CYP3A4-substrate:  0.284

ADMET: Excretion

Clearance (CL):  1.411
Half-life (T1/2):  0.096

ADMET: Toxicity

hERG Blockers:  0.04
Human Hepatotoxicity (H-HT):  0.955
Drug-inuced Liver Injury (DILI):  0.874
AMES Toxicity:  0.001
Rat Oral Acute Toxicity:  0.333
Maximum Recommended Daily Dose:  0.982
Skin Sensitization:  0.307
Carcinogencity:  0.744
Eye Corrosion:  0.003
Eye Irritation:  0.009
Respiratory Toxicity:  0.948

Download Data

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

  Natural Product: NPC476921

Natural Product ID:  NPC476921
Common Name*:   sodium;[(E)-[(1R,4aR,4bS,8aS,10aS)-1-[2-[1-[(1S)-1-carboxy-2-methylpropyl]-5-oxo-2H-pyrrol-3-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-[(1S)-1-carboxy-2-methylpropyl]-5-oxo-2H-pyrrol-3-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:  ZCEAEHBMGXVYKZ-QFFBPWKRSA-M
Standard InCHI:  InChI=1S/C30H47NO7S.Na/c1-19(2)26(27(33)34)31-17-20(16-25(31)32)8-10-22-21(18-38-39(35,36)37)9-11-24-29(22,5)15-12-23-28(3,4)13-7-14-30(23,24)6;/h16,18-19,22-24,26H,7-15,17H2,1-6H3,(H,33,34)(H,35,36,37);/q;+1/p-1/b21-18+;/t22-,23-,24-,26-,29+,30-;/m0./s1
SMILES:  CC(C)[C@@H](C(=O)O)N1CC(=CC1=O)CC[C@H]2/C(=C/OS(=O)(=O)[O-])/CC[C@H]3[C@@]2(CC[C@@H]4[C@@]3(CCCC4(C)C)C)C.[Na+]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   90683095
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 = 1.9 ug/ml PMID[24828374]
NPT111 Cell Line K562 Homo sapiens LC50 = 3.9 ug/ml PMID[24828374]
NPT2 Others Unspecified MIC = 27 ug/ml PMID[24828374]
NPT2 Others Unspecified MIC = 64 ug/ml PMID[24828374]
NPT1190 Organism Salmonella enterica Salmonella enterica MIC = 100 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]
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 NPC476921 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
0.95 High Similarity NPC476918
0.93 High Similarity NPC476926
0.8 Intermediate Similarity NPC476922
0.7905 Intermediate Similarity NPC477964
0.789 Intermediate Similarity NPC476920
0.7568 Intermediate Similarity NPC476276
0.7568 Intermediate Similarity NPC476919
0.7545 Intermediate Similarity NPC476328
0.7255 Intermediate Similarity NPC157479
0.7157 Intermediate Similarity NPC147513
0.7143 Intermediate Similarity NPC17143
0.7143 Intermediate Similarity NPC47230
0.6917 Remote Similarity NPC477121
0.6875 Remote Similarity NPC77703
0.6863 Remote Similarity NPC215474
0.68 Remote Similarity NPC321197
0.6765 Remote Similarity NPC90150
0.675 Remote Similarity NPC145501
0.6695 Remote Similarity NPC63511
0.6638 Remote Similarity NPC185929
0.6636 Remote Similarity NPC324405
0.6579 Remote Similarity NPC474001
0.6545 Remote Similarity NPC93027
0.6509 Remote Similarity NPC311769
0.6509 Remote Similarity NPC182106
0.6415 Remote Similarity NPC318515
0.641 Remote Similarity NPC469604
0.6393 Remote Similarity NPC469597
0.6387 Remote Similarity NPC24596
0.6379 Remote Similarity NPC474244
0.6364 Remote Similarity NPC474411
0.6364 Remote Similarity NPC474431
0.6348 Remote Similarity NPC26597
0.633 Remote Similarity NPC259252
0.632 Remote Similarity NPC474006
0.6281 Remote Similarity NPC469603
0.6271 Remote Similarity NPC470596
0.625 Remote Similarity NPC474099
0.6239 Remote Similarity NPC43308
0.6218 Remote Similarity NPC86906
0.6198 Remote Similarity NPC218602
0.6195 Remote Similarity NPC476754
0.6179 Remote Similarity NPC80834
0.6179 Remote Similarity NPC469968
0.6174 Remote Similarity NPC184033
0.6168 Remote Similarity NPC477124
0.6154 Remote Similarity NPC188785
0.6154 Remote Similarity NPC39473
0.6147 Remote Similarity NPC322672
0.6121 Remote Similarity NPC140685
0.6116 Remote Similarity NPC470595
0.6102 Remote Similarity NPC226509
0.6102 Remote Similarity NPC152718
0.6091 Remote Similarity NPC473525
0.6087 Remote Similarity NPC325960
0.6087 Remote Similarity NPC319692
0.6083 Remote Similarity NPC195841
0.6083 Remote Similarity NPC233256
0.608 Remote Similarity NPC176336
0.6055 Remote Similarity NPC75810
0.6055 Remote Similarity NPC319913
0.6053 Remote Similarity NPC324078
0.6048 Remote Similarity NPC474452
0.604 Remote Similarity NPC265789
0.6034 Remote Similarity NPC52820
0.6017 Remote Similarity NPC34193
0.6016 Remote Similarity NPC472313
0.6 Remote Similarity NPC475239
0.6 Remote Similarity NPC478137
0.6 Remote Similarity NPC119329
0.6 Remote Similarity NPC469958
0.5968 Remote Similarity NPC79238
0.5968 Remote Similarity NPC474459
0.5966 Remote Similarity NPC58200
0.5965 Remote Similarity NPC476753
0.5965 Remote Similarity NPC476752
0.5965 Remote Similarity NPC247316
0.5948 Remote Similarity NPC247220
0.5948 Remote Similarity NPC476903
0.5926 Remote Similarity NPC473810
0.5917 Remote Similarity NPC68001
0.5917 Remote Similarity NPC199831
0.5917 Remote Similarity NPC474828
0.5917 Remote Similarity NPC474827
0.5897 Remote Similarity NPC140300
0.5882 Remote Similarity NPC21773
0.5878 Remote Similarity NPC472458
0.5856 Remote Similarity NPC166458
0.584 Remote Similarity NPC143173
0.5833 Remote Similarity NPC50815
0.5833 Remote Similarity NPC476755
0.5833 Remote Similarity NPC247060
0.5825 Remote Similarity NPC144947
0.582 Remote Similarity NPC258130
0.582 Remote Similarity NPC55462
0.582 Remote Similarity NPC230677
0.5812 Remote Similarity NPC289140
0.581 Remote Similarity NPC7214
0.5804 Remote Similarity NPC324506
0.5802 Remote Similarity NPC242692
0.5798 Remote Similarity NPC128698
0.5798 Remote Similarity NPC239768
0.5794 Remote Similarity NPC211322
0.5789 Remote Similarity NPC53240
0.5789 Remote Similarity NPC473056
0.5789 Remote Similarity NPC84171
0.5784 Remote Similarity NPC473442
0.5784 Remote Similarity NPC120167
0.5781 Remote Similarity NPC246904
0.578 Remote Similarity NPC142683
0.5776 Remote Similarity NPC477290
0.5772 Remote Similarity NPC25340
0.5769 Remote Similarity NPC168975
0.5769 Remote Similarity NPC75485
0.5769 Remote Similarity NPC476904
0.5766 Remote Similarity NPC34811
0.5766 Remote Similarity NPC152684
0.5766 Remote Similarity NPC474013
0.5766 Remote Similarity NPC30984
0.5763 Remote Similarity NPC292819
0.5763 Remote Similarity NPC4834
0.576 Remote Similarity NPC328052
0.576 Remote Similarity NPC72688
0.5741 Remote Similarity NPC104545
0.5739 Remote Similarity NPC477122
0.5727 Remote Similarity NPC21667
0.5726 Remote Similarity NPC220730
0.5714 Remote Similarity NPC44733
0.5714 Remote Similarity NPC91604
0.5714 Remote Similarity NPC58281
0.5703 Remote Similarity NPC476814
0.5703 Remote Similarity NPC472536
0.5703 Remote Similarity NPC476813
0.5703 Remote Similarity NPC103391
0.5702 Remote Similarity NPC174342
0.5702 Remote Similarity NPC471654
0.5702 Remote Similarity NPC477973
0.5702 Remote Similarity NPC249312
0.5702 Remote Similarity NPC471083
0.5701 Remote Similarity NPC280654
0.5701 Remote Similarity NPC260385
0.5701 Remote Similarity NPC110094
0.5691 Remote Similarity NPC36497
0.5688 Remote Similarity NPC471898
0.5688 Remote Similarity NPC278459
0.5686 Remote Similarity NPC90782
0.5682 Remote Similarity NPC470277
0.568 Remote Similarity NPC470536
0.5678 Remote Similarity NPC9487
0.5676 Remote Similarity NPC96095
0.5676 Remote Similarity NPC248758
0.5676 Remote Similarity NPC477289
0.5676 Remote Similarity NPC25833
0.5669 Remote Similarity NPC56796
0.5667 Remote Similarity NPC474985
0.5662 Remote Similarity NPC478136
0.566 Remote Similarity NPC474463
0.5659 Remote Similarity NPC288629
0.5656 Remote Similarity NPC474563
0.5656 Remote Similarity NPC241879
0.5652 Remote Similarity NPC120335
0.5649 Remote Similarity NPC35037
0.5648 Remote Similarity NPC199595
0.5645 Remote Similarity NPC169375
0.5636 Remote Similarity NPC320514
0.5636 Remote Similarity NPC200513
0.5635 Remote Similarity NPC476290
0.5631 Remote Similarity NPC97614
0.563 Remote Similarity NPC237286
0.563 Remote Similarity NPC91036
0.563 Remote Similarity NPC309525
0.563 Remote Similarity NPC474164
0.5625 Remote Similarity NPC60350
0.5625 Remote Similarity NPC76283
0.5625 Remote Similarity NPC2709
0.5625 Remote Similarity NPC65661
0.562 Remote Similarity NPC474348
0.5619 Remote Similarity NPC211641
0.5615 Remote Similarity NPC473573
0.5614 Remote Similarity NPC472302
0.561 Remote Similarity NPC477000
0.561 Remote Similarity NPC477001
0.5607 Remote Similarity NPC471899
0.5607 Remote Similarity NPC107039
0.5607 Remote Similarity NPC471897
0.5607 Remote Similarity NPC472300
0.5603 Remote Similarity NPC23217
0.5603 Remote Similarity NPC329842
0.5603 Remote Similarity NPC65120
0.5603 Remote Similarity NPC145707
0.5603 Remote Similarity NPC4036
0.5603 Remote Similarity NPC145067
0.5603 Remote Similarity NPC472264
0.5603 Remote Similarity NPC158030
0.5603 Remote Similarity NPC233455
0.5603 Remote Similarity NPC230064
0.5603 Remote Similarity NPC476064
0.56 Remote Similarity NPC207820
0.56 Remote Similarity NPC159367
0.56 Remote Similarity NPC140251

  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 NPC476921 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
0.6518 Remote Similarity NPD5349 Clinical (unspecified phase)
0.6083 Remote Similarity NPD7333 Discontinued
0.6047 Remote Similarity NPD6909 Approved
0.6047 Remote Similarity NPD6908 Approved
0.6 Remote Similarity NPD1376 Discontinued
0.5676 Remote Similarity NPD3668 Phase 3
0.5669 Remote Similarity NPD8078 Approved
0.5669 Remote Similarity NPD8077 Approved
0.5636 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5614 Remote Similarity NPD7513 Clinical (unspecified phase)
0.5614 Remote Similarity NPD5737 Approved
0.5614 Remote Similarity NPD6672 Approved
0.5603 Remote Similarity NPD7515 Phase 2

  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