Structure

Physi-Chem Properties

Molecular Weight:  454.33
Volume:  501.547
LogP:  4.164
LogD:  4.181
LogS:  -4.73
# Rotatable Bonds:  12
TPSA:  58.44
# H-Bond Aceptor:  6
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.297
Synthetic Accessibility Score:  3.527
Fsp3:  0.593
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.992
MDCK Permeability:  2.016684265981894e-05
Pgp-inhibitor:  0.484
Pgp-substrate:  0.011
Human Intestinal Absorption (HIA):  0.914
20% Bioavailability (F20%):  0.053
30% Bioavailability (F30%):  0.955

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.896
Plasma Protein Binding (PPB):  91.39490509033203%
Volume Distribution (VD):  1.438
Pgp-substrate:  4.090315341949463%

ADMET: Metabolism

CYP1A2-inhibitor:  0.061
CYP1A2-substrate:  0.145
CYP2C19-inhibitor:  0.931
CYP2C19-substrate:  0.542
CYP2C9-inhibitor:  0.907
CYP2C9-substrate:  0.974
CYP2D6-inhibitor:  0.557
CYP2D6-substrate:  0.698
CYP3A4-inhibitor:  0.82
CYP3A4-substrate:  0.1

ADMET: Excretion

Clearance (CL):  4.392
Half-life (T1/2):  0.516

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.92
Drug-inuced Liver Injury (DILI):  0.845
AMES Toxicity:  0.029
Rat Oral Acute Toxicity:  0.004
Maximum Recommended Daily Dose:  0.911
Skin Sensitization:  0.951
Carcinogencity:  0.47
Eye Corrosion:  0.003
Eye Irritation:  0.031
Respiratory Toxicity:  0.903

Download Data

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

  Natural Product: NPC226184

Natural Product ID:  NPC226184
Common Name*:   Nuttigin E
IUPAC Name:   1,3-dimethyl-7-[(2E,6E,11Z)-3,7,11,15-tetramethyl-13-oxohexadeca-2,6,11-trienyl]-2H-purin-6-one
Synonyms:   Nuttigin E
Standard InCHIKey:  VVFKJCSQWFALCI-FGVXUPOYSA-N
Standard InCHI:  InChI=1S/C27H42N4O2/c1-20(2)16-24(32)17-23(5)13-9-11-21(3)10-8-12-22(4)14-15-31-18-28-26-25(31)27(33)30(7)19-29(26)6/h10,14,17-18,20H,8-9,11-13,15-16,19H2,1-7H3/b21-10+,22-14+,23-17-
SMILES:  CC(C)CC(=O)/C=C(/C)CCC/C(=C/CC/C(=C/Cn1cnc2c1C(=O)N(C)CN2C)/C)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL229208
PubChem CID:   16756547
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids

*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
NPO3303 Euplexaura nuttingi Species Plexauridae Eukaryota n.a. Tanzanian n.a. PMID[17571903]
NPO3303 Euplexaura nuttingi Species Plexauridae Eukaryota 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
NPT111 Cell Line K562 Homo sapiens Inhibition = 30.0 % PMID[458551]
NPT5430 Cell Line UT7 Homo sapiens Inhibition = 50.0 % PMID[458551]

☑ 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 NPC226184 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 NPC76544
0.9845 High Similarity NPC167285
0.7769 Intermediate Similarity NPC256849
0.7591 Intermediate Similarity NPC109322
0.7536 Intermediate Similarity NPC180493
0.7532 Intermediate Similarity NPC472833
0.7389 Intermediate Similarity NPC472832
0.7389 Intermediate Similarity NPC18308
0.7368 Intermediate Similarity NPC303899
0.7348 Intermediate Similarity NPC47936
0.7174 Intermediate Similarity NPC252603
0.7132 Intermediate Similarity NPC148385
0.7068 Intermediate Similarity NPC75131
0.7 Intermediate Similarity NPC296437
0.6954 Remote Similarity NPC470266
0.6863 Remote Similarity NPC476433
0.6863 Remote Similarity NPC476528
0.6818 Remote Similarity NPC476522
0.6818 Remote Similarity NPC476520
0.6818 Remote Similarity NPC476013
0.6818 Remote Similarity NPC474986
0.6813 Remote Similarity NPC472834
0.6795 Remote Similarity NPC476408
0.6786 Remote Similarity NPC278549
0.6774 Remote Similarity NPC476521
0.6738 Remote Similarity NPC158847
0.6584 Remote Similarity NPC321052
0.6454 Remote Similarity NPC199790
0.6235 Remote Similarity NPC244700
0.6232 Remote Similarity NPC476099
0.6204 Remote Similarity NPC476561
0.6089 Remote Similarity NPC473585
0.6067 Remote Similarity NPC477119
0.6044 Remote Similarity NPC477118
0.6011 Remote Similarity NPC477120
0.5965 Remote Similarity NPC124276
0.5964 Remote Similarity NPC326694
0.5956 Remote Similarity NPC265111
0.5887 Remote Similarity NPC476562
0.586 Remote Similarity NPC57279
0.5854 Remote Similarity NPC89139
0.5845 Remote Similarity NPC119133
0.5833 Remote Similarity NPC164845
0.5793 Remote Similarity NPC217656
0.5784 Remote Similarity NPC476341
0.5758 Remote Similarity NPC116555
0.5732 Remote Similarity NPC8590
0.5732 Remote Similarity NPC246193
0.5722 Remote Similarity NPC527
0.5722 Remote Similarity NPC133782
0.5722 Remote Similarity NPC144474
0.5679 Remote Similarity NPC33996
0.5674 Remote Similarity NPC87981
0.5674 Remote Similarity NPC174114
0.5665 Remote Similarity NPC239737
0.5644 Remote Similarity NPC210947
0.5644 Remote Similarity NPC129756
0.564 Remote Similarity NPC217021
0.564 Remote Similarity NPC470679
0.564 Remote Similarity NPC469975
0.5615 Remote Similarity NPC101676

  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 NPC226184 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
0.8244 Intermediate Similarity NPD2221 Clinical (unspecified phase)
0.8231 Intermediate Similarity NPD580 Discontinued
0.8209 Intermediate Similarity NPD1775 Approved
0.8209 Intermediate Similarity NPD1085 Approved
0.7769 Intermediate Similarity NPD9359 Approved
0.7769 Intermediate Similarity NPD9358 Approved
0.7744 Intermediate Similarity NPD578 Discontinued
0.7724 Intermediate Similarity NPD2253 Discontinued
0.7647 Intermediate Similarity NPD4262 Discontinued
0.7626 Intermediate Similarity NPD1127 Approved
0.7626 Intermediate Similarity NPD1128 Approved
0.7609 Intermediate Similarity NPD281 Approved
0.7552 Intermediate Similarity NPD1119 Phase 2
0.7536 Intermediate Similarity NPD9544 Approved
0.7536 Intermediate Similarity NPD78 Approved
0.7536 Intermediate Similarity NPD579 Clinical (unspecified phase)
0.7439 Intermediate Similarity NPD3041 Approved
0.7432 Intermediate Similarity NPD2179 Discontinued
0.7432 Intermediate Similarity NPD1117 Clinical (unspecified phase)
0.7351 Intermediate Similarity NPD7531 Clinical (unspecified phase)
0.7343 Intermediate Similarity NPD282 Approved
0.7174 Intermediate Similarity NPD9289 Approved
0.7174 Intermediate Similarity NPD9288 Approved
0.7174 Intermediate Similarity NPD76 Approved
0.7174 Intermediate Similarity NPD9292 Approved
0.7126 Intermediate Similarity NPD4155 Approved
0.7027 Intermediate Similarity NPD535 Approved
0.7007 Intermediate Similarity NPD9086 Approved
0.6968 Remote Similarity NPD4182 Phase 3
0.6968 Remote Similarity NPD4183 Phase 3
0.6906 Remote Similarity NPD6837 Clinical (unspecified phase)
0.6879 Remote Similarity NPD9290 Approved
0.6732 Remote Similarity NPD1118 Discontinued
0.6646 Remote Similarity NPD5321 Phase 3
0.6594 Remote Similarity NPD8954 Approved
0.6594 Remote Similarity NPD8955 Approved
0.6593 Remote Similarity NPD1952 Discontinued
0.6592 Remote Similarity NPD1658 Discontinued
0.6429 Remote Similarity NPD3460 Discontinued
0.6416 Remote Similarity NPD7297 Phase 2
0.64 Remote Similarity NPD3432 Approved
0.6368 Remote Similarity NPD3839 Phase 2
0.6368 Remote Similarity NPD3840 Phase 2
0.6302 Remote Similarity NPD2819 Clinical (unspecified phase)
0.6298 Remote Similarity NPD1250 Clinical (unspecified phase)
0.6289 Remote Similarity NPD3706 Clinical (unspecified phase)
0.6271 Remote Similarity NPD5508 Phase 1
0.6264 Remote Similarity NPD3081 Clinical (unspecified phase)
0.6257 Remote Similarity NPD8121 Phase 3
0.6257 Remote Similarity NPD8120 Approved
0.6238 Remote Similarity NPD5887 Clinical (unspecified phase)
0.623 Remote Similarity NPD6271 Approved
0.6218 Remote Similarity NPD2602 Clinical (unspecified phase)
0.6186 Remote Similarity NPD4048 Approved
0.6162 Remote Similarity NPD460 Discontinued
0.6142 Remote Similarity NPD4395 Phase 1
0.6133 Remote Similarity NPD1308 Approved
0.6131 Remote Similarity NPD5969 Clinical (unspecified phase)
0.6114 Remote Similarity NPD3347 Clinical (unspecified phase)
0.6114 Remote Similarity NPD1506 Discontinued
0.6108 Remote Similarity NPD3430 Approved
0.6108 Remote Similarity NPD3431 Approved
0.605 Remote Similarity NPD4541 Clinical (unspecified phase)
0.6029 Remote Similarity NPD3042 Approved
0.6029 Remote Similarity NPD3043 Approved
0.6022 Remote Similarity NPD3586 Phase 2
0.6011 Remote Similarity NPD7023 Clinical (unspecified phase)
0.601 Remote Similarity NPD2363 Discontinued
0.6 Remote Similarity NPD2442 Approved
0.6 Remote Similarity NPD2443 Approved
0.6 Remote Similarity NPD875 Clinical (unspecified phase)
0.5978 Remote Similarity NPD6418 Phase 1
0.597 Remote Similarity NPD1623 Approved
0.5969 Remote Similarity NPD2408 Discontinued
0.5952 Remote Similarity NPD8159 Discontinued
0.595 Remote Similarity NPD2412 Clinical (unspecified phase)
0.5949 Remote Similarity NPD3905 Phase 3
0.5949 Remote Similarity NPD576 Discontinued
0.5936 Remote Similarity NPD5973 Phase 2
0.5936 Remote Similarity NPD5974 Approved
0.593 Remote Similarity NPD516 Clinical (unspecified phase)
0.5928 Remote Similarity NPD6229 Phase 2
0.5926 Remote Similarity NPD3362 Clinical (unspecified phase)
0.5924 Remote Similarity NPD1058 Discontinued
0.592 Remote Similarity NPD5643 Phase 2
0.5909 Remote Similarity NPD1354 Approved
0.5909 Remote Similarity NPD1355 Clinical (unspecified phase)
0.5909 Remote Similarity NPD1356 Approved
0.5909 Remote Similarity NPD4863 Approved
0.5907 Remote Similarity NPD2879 Approved
0.5907 Remote Similarity NPD2881 Approved
0.589 Remote Similarity NPD4240 Approved
0.5882 Remote Similarity NPD4892 Clinical (unspecified phase)
0.586 Remote Similarity NPD5016 Approved
0.5854 Remote Similarity NPD7158 Phase 1
0.5845 Remote Similarity NPD9291 Approved
0.5843 Remote Similarity NPD3105 Discontinued
0.5838 Remote Similarity NPD6520 Phase 3
0.5838 Remote Similarity NPD6521 Phase 3
0.5833 Remote Similarity NPD1705 Discontinued
0.5829 Remote Similarity NPD5685 Approved
0.5829 Remote Similarity NPD5686 Approved
0.5818 Remote Similarity NPD1730 Discontinued
0.5813 Remote Similarity NPD6470 Phase 3
0.5808 Remote Similarity NPD1600 Suspended
0.5808 Remote Similarity NPD4709 Approved
0.5803 Remote Similarity NPD7108 Phase 3
0.5803 Remote Similarity NPD7107 Phase 3
0.5802 Remote Similarity NPD4764 Approved
0.5802 Remote Similarity NPD4765 Approved
0.5797 Remote Similarity NPD4132 Clinical (unspecified phase)
0.5795 Remote Similarity NPD1313 Approved
0.5793 Remote Similarity NPD566 Approved
0.5793 Remote Similarity NPD567 Approved
0.5793 Remote Similarity NPD568 Approved
0.5774 Remote Similarity NPD3708 Phase 2
0.5771 Remote Similarity NPD7557 Clinical (unspecified phase)
0.5769 Remote Similarity NPD9633 Phase 3
0.5765 Remote Similarity NPD4446 Approved
0.5762 Remote Similarity NPD2400 Phase 2
0.5756 Remote Similarity NPD6210 Phase 3
0.5749 Remote Similarity NPD775 Approved
0.5744 Remote Similarity NPD4924 Clinical (unspecified phase)
0.5743 Remote Similarity NPD757 Phase 3
0.5742 Remote Similarity NPD515 Phase 1
0.574 Remote Similarity NPD7842 Phase 2
0.5733 Remote Similarity NPD9360 Approved
0.5729 Remote Similarity NPD3860 Discontinued
0.5723 Remote Similarity NPD3678 Phase 2
0.5706 Remote Similarity NPD3695 Approved
0.5706 Remote Similarity NPD3696 Approved
0.5705 Remote Similarity NPD870 Clinical (unspecified phase)
0.569 Remote Similarity NPD1335 Approved
0.5689 Remote Similarity NPD2873 Approved
0.5686 Remote Similarity NPD1591 Approved
0.5685 Remote Similarity NPD2130 Discontinued
0.5685 Remote Similarity NPD4299 Phase 1
0.5679 Remote Similarity NPD1808 Phase 1
0.5677 Remote Similarity NPD9408 Phase 3
0.5668 Remote Similarity NPD4940 Approved
0.5667 Remote Similarity NPD1368 Approved
0.5665 Remote Similarity NPD2604 Approved
0.5664 Remote Similarity NPD9626 Clinical (unspecified phase)
0.5663 Remote Similarity NPD9627 Approved
0.5657 Remote Similarity NPD2008 Discontinued
0.5652 Remote Similarity NPD1120 Approved
0.5652 Remote Similarity NPD1121 Approved
0.564 Remote Similarity NPD3612 Phase 2
0.564 Remote Similarity NPD7887 Approved
0.564 Remote Similarity NPD7888 Approved
0.564 Remote Similarity NPD2524 Discontinued
0.5638 Remote Similarity NPD2009 Clinical (unspecified phase)
0.5636 Remote Similarity NPD2618 Phase 1
0.5633 Remote Similarity NPD248 Discontinued
0.5625 Remote Similarity NPD2593 Clinical (unspecified phase)
0.5621 Remote Similarity NPD1690 Clinical (unspecified phase)
0.5614 Remote Similarity NPD9605 Phase 3
0.5602 Remote Similarity NPD174 Discontinued

  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