Structure

Physi-Chem Properties

Molecular Weight:  580.37
Volume:  597.668
LogP:  3.448
LogD:  3.329
LogS:  -2.779
# Rotatable Bonds:  15
TPSA:  153.16
# H-Bond Aceptor:  9
# H-Bond Donor:  6
# Rings:  3
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.069
Synthetic Accessibility Score:  4.759
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:  -5.401
MDCK Permeability:  8.08094409876503e-06
Pgp-inhibitor:  0.394
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.06
20% Bioavailability (F20%):  0.994
30% Bioavailability (F30%):  0.587

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.832
Plasma Protein Binding (PPB):  96.34029388427734%
Volume Distribution (VD):  1.177
Pgp-substrate:  2.132502794265747%

ADMET: Metabolism

CYP1A2-inhibitor:  0.008
CYP1A2-substrate:  0.246
CYP2C19-inhibitor:  0.01
CYP2C19-substrate:  0.052
CYP2C9-inhibitor:  0.025
CYP2C9-substrate:  0.039
CYP2D6-inhibitor:  0.748
CYP2D6-substrate:  0.673
CYP3A4-inhibitor:  0.077
CYP3A4-substrate:  0.046

ADMET: Excretion

Clearance (CL):  5.312
Half-life (T1/2):  0.014

ADMET: Toxicity

hERG Blockers:  0.54
Human Hepatotoxicity (H-HT):  0.545
Drug-inuced Liver Injury (DILI):  0.041
AMES Toxicity:  0.024
Rat Oral Acute Toxicity:  0.874
Maximum Recommended Daily Dose:  0.945
Skin Sensitization:  0.616
Carcinogencity:  0.732
Eye Corrosion:  0.003
Eye Irritation:  0.008
Respiratory Toxicity:  0.97

Download Data

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

  Natural Product: NPC477121

Natural Product ID:  NPC477121
Common Name*:   [2-[2-[(1S,2S,4aR)-1,2,5,5-tetramethyl-2,3,4,4a,6,7-hexahydronaphthalen-1-yl]ethyl]-5-[1-[4-(diaminomethylideneamino)butyl]-5-oxo-2H-pyrrol-4-yl]pentyl] hydrogen sulfate
IUPAC Name:   [2-[2-[(1S,2S,4aR)-1,2,5,5-tetramethyl-2,3,4,4a,6,7-hexahydronaphthalen-1-yl]ethyl]-5-[1-[4-(diaminomethylideneamino)butyl]-5-oxo-2H-pyrrol-4-yl]pentyl] hydrogen sulfate
Synonyms:   Fasciospongine C
Standard InCHIKey:  QFJUUZMSENDBFD-HMDKUDOWSA-N
Standard InCHI:  InChI=1S/C30H52N4O5S/c1-22-12-13-25-26(11-8-16-29(25,2)3)30(22,4)17-14-23(21-39-40(36,37)38)9-7-10-24-15-20-34(27(24)35)19-6-5-18-33-28(31)32/h11,15,22-23,25H,5-10,12-14,16-21H2,1-4H3,(H4,31,32,33)(H,36,37,38)/t22-,23?,25-,30-/m0/s1
SMILES:  C[C@H]1CC[C@H]2C(=CCCC2(C)C)[C@@]1(C)CCC(CCCC3=CCN(C3=O)CCCCN=C(N)N)COS(=O)(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   25242869
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000403] Organic sulfuric acids and derivatives
        • [CHEMONTID:0003455] Sulfuric acid esters
          • [CHEMONTID:0001185] Sulfuric acid monoesters

*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
NPO33581 Fasciospongia sp. Species Thorectidae Eukaryota n.a. at a depth of 1 m in Palau 2003-DEC PMID[19178162]

☑ 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
NPT447 Organism Streptomyces Streptomyces IZ = 14 mm PMID[19178162]
NPT447 Organism Streptomyces Streptomyces IZ = 13 mm PMID[19178162]

☑ 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 NPC477121 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
0.8598 High Similarity NPC477964
0.7288 Intermediate Similarity NPC476926
0.7167 Intermediate Similarity NPC476920
0.7167 Intermediate Similarity NPC476918
0.7094 Intermediate Similarity NPC77703
0.6917 Remote Similarity NPC476921
0.6885 Remote Similarity NPC476919
0.6748 Remote Similarity NPC476276
0.6721 Remote Similarity NPC476328
0.6667 Remote Similarity NPC476922
0.6466 Remote Similarity NPC47230
0.6466 Remote Similarity NPC17143
0.6424 Remote Similarity NPC477118
0.6386 Remote Similarity NPC477120
0.6378 Remote Similarity NPC63511
0.632 Remote Similarity NPC195841
0.632 Remote Similarity NPC233256
0.6288 Remote Similarity NPC474006
0.6276 Remote Similarity NPC477399
0.6276 Remote Similarity NPC477401
0.6269 Remote Similarity NPC314293
0.625 Remote Similarity NPC328052
0.619 Remote Similarity NPC230677
0.6183 Remote Similarity NPC176336
0.6167 Remote Similarity NPC476754
0.6154 Remote Similarity NPC324405
0.6129 Remote Similarity NPC34193
0.6083 Remote Similarity NPC93027
0.6061 Remote Similarity NPC477119
0.6061 Remote Similarity NPC145501
0.605 Remote Similarity NPC84171
0.6047 Remote Similarity NPC175585
0.6042 Remote Similarity NPC477400
0.6032 Remote Similarity NPC98765
0.6032 Remote Similarity NPC474563
0.6031 Remote Similarity NPC124358
0.6014 Remote Similarity NPC321197
0.6 Remote Similarity NPC476290
0.6 Remote Similarity NPC474001
0.5985 Remote Similarity NPC469597
0.5983 Remote Similarity NPC157479
0.5969 Remote Similarity NPC307903
0.5969 Remote Similarity NPC24596
0.5969 Remote Similarity NPC140251
0.5954 Remote Similarity NPC474411
0.5954 Remote Similarity NPC79238
0.5954 Remote Similarity NPC474431
0.5952 Remote Similarity NPC58200
0.595 Remote Similarity NPC476752
0.595 Remote Similarity NPC476753
0.5948 Remote Similarity NPC25833
0.5935 Remote Similarity NPC247220
0.5929 Remote Similarity NPC96010
0.5929 Remote Similarity NPC317654
0.592 Remote Similarity NPC135799
0.592 Remote Similarity NPC128698
0.592 Remote Similarity NPC239768
0.5913 Remote Similarity NPC215474
0.5909 Remote Similarity NPC7797
0.5909 Remote Similarity NPC476269
0.5897 Remote Similarity NPC147513
0.5891 Remote Similarity NPC244982
0.5891 Remote Similarity NPC476756
0.5887 Remote Similarity NPC184033
0.5887 Remote Similarity NPC478136
0.5887 Remote Similarity NPC474164
0.5882 Remote Similarity NPC35037
0.5878 Remote Similarity NPC72688
0.5878 Remote Similarity NPC472313
0.5873 Remote Similarity NPC118275
0.5862 Remote Similarity NPC477124
0.586 Remote Similarity NPC477398
0.5845 Remote Similarity NPC324722
0.5845 Remote Similarity NPC198644
0.5845 Remote Similarity NPC311244
0.5827 Remote Similarity NPC176012
0.5827 Remote Similarity NPC152718
0.5827 Remote Similarity NPC226509
0.5827 Remote Similarity NPC469598
0.582 Remote Similarity NPC475255
0.5814 Remote Similarity NPC185929
0.5798 Remote Similarity NPC43308
0.5789 Remote Similarity NPC474452
0.5776 Remote Similarity NPC328351
0.5769 Remote Similarity NPC475800
0.5763 Remote Similarity NPC182106
0.5763 Remote Similarity NPC311769
0.5763 Remote Similarity NPC189311
0.5739 Remote Similarity NPC2482
0.5736 Remote Similarity NPC475239
0.5736 Remote Similarity NPC469958
0.5736 Remote Similarity NPC119329
0.5735 Remote Similarity NPC476190
0.5735 Remote Similarity NPC216335
0.5726 Remote Similarity NPC21667
0.5726 Remote Similarity NPC97913
0.5726 Remote Similarity NPC161344
0.5726 Remote Similarity NPC307258
0.5725 Remote Similarity NPC159367
0.5725 Remote Similarity NPC207820
0.5714 Remote Similarity NPC474459
0.5714 Remote Similarity NPC44733
0.5702 Remote Similarity NPC174342
0.5702 Remote Similarity NPC5509
0.5692 Remote Similarity NPC477292
0.5691 Remote Similarity NPC247316
0.569 Remote Similarity NPC116797
0.569 Remote Similarity NPC278459
0.5683 Remote Similarity NPC470277
0.5682 Remote Similarity NPC474725
0.568 Remote Similarity NPC325960
0.568 Remote Similarity NPC319692
0.5678 Remote Similarity NPC472865
0.5678 Remote Similarity NPC164577
0.5678 Remote Similarity NPC214043
0.5678 Remote Similarity NPC473246
0.5678 Remote Similarity NPC85774
0.5672 Remote Similarity NPC477291
0.5667 Remote Similarity NPC93778
0.5662 Remote Similarity NPC288629
0.5658 Remote Similarity NPC142761
0.5652 Remote Similarity NPC327674
0.5649 Remote Similarity NPC467022
0.5641 Remote Similarity NPC103486
0.5641 Remote Similarity NPC200513
0.563 Remote Similarity NPC2709
0.563 Remote Similarity NPC469948
0.563 Remote Similarity NPC65661
0.563 Remote Similarity NPC75810
0.5625 Remote Similarity NPC45830
0.5625 Remote Similarity NPC243106
0.562 Remote Similarity NPC226863
0.562 Remote Similarity NPC259252
0.5615 Remote Similarity NPC87919
0.5606 Remote Similarity NPC220730
0.5603 Remote Similarity NPC472478

  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 NPC477121 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
0.5948 Remote Similarity NPD3668 Phase 3
0.5938 Remote Similarity NPD7333 Discontinued
0.5935 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5917 Remote Similarity NPD790 Approved
0.5915 Remote Similarity NPD6914 Discontinued
0.5694 Remote Similarity NPD7751 Phase 1
0.5683 Remote Similarity NPD7739 Clinical (unspecified phase)
0.5641 Remote Similarity NPD4752 Clinical (unspecified phase)

  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