Structure

Physi-Chem Properties

Molecular Weight:  405.25
Volume:  436.937
LogP:  4.015
LogD:  3.518
LogS:  -3.697
# Rotatable Bonds:  14
TPSA:  99.76
# H-Bond Aceptor:  6
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.371
Synthetic Accessibility Score:  3.559
Fsp3:  0.565
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -5.779
MDCK Permeability:  4.810671271116007e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.909
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.007

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.003
Plasma Protein Binding (PPB):  96.24163055419922%
Volume Distribution (VD):  0.214
Pgp-substrate:  0.7125352025032043%

ADMET: Metabolism

CYP1A2-inhibitor:  0.046
CYP1A2-substrate:  0.082
CYP2C19-inhibitor:  0.022
CYP2C19-substrate:  0.049
CYP2C9-inhibitor:  0.343
CYP2C9-substrate:  0.995
CYP2D6-inhibitor:  0.106
CYP2D6-substrate:  0.229
CYP3A4-inhibitor:  0.021
CYP3A4-substrate:  0.02

ADMET: Excretion

Clearance (CL):  2.376
Half-life (T1/2):  0.855

ADMET: Toxicity

hERG Blockers:  0.007
Human Hepatotoxicity (H-HT):  0.857
Drug-inuced Liver Injury (DILI):  0.677
AMES Toxicity:  0.001
Rat Oral Acute Toxicity:  0.012
Maximum Recommended Daily Dose:  0.082
Skin Sensitization:  0.859
Carcinogencity:  0.033
Eye Corrosion:  0.024
Eye Irritation:  0.087
Respiratory Toxicity:  0.036

Download Data

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

  Natural Product: NPC17143

Natural Product ID:  NPC17143
Common Name*:   Ent-Ircinialactam C
IUPAC Name:   (3R,7E,11E)-14-[1-(carboxymethyl)-5-oxo-2H-pyrrol-4-yl]-3,7,11-trimethyltetradeca-7,11-dienoic acid
Synonyms:   Ent-Ircinialactam C
Standard InCHIKey:  FYWCTUYAFXXJQJ-CVUGZRRRSA-N
Standard InCHI:  InChI=1S/C23H35NO5/c1-17(9-5-11-19(3)15-21(25)26)7-4-8-18(2)10-6-12-20-13-14-24(23(20)29)16-22(27)28/h7,10,13,19H,4-6,8-9,11-12,14-16H2,1-3H3,(H,25,26)(H,27,28)/b17-7+,18-10+/t19-/m1/s1
SMILES:  C/C(=CCC/C(=C/CCC1=CCN(CC(=O)O)C1=O)/C)/CCC[C@@H](C)CC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1092618
PubChem CID:   46886221
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
NPO33253 Irciniidae Family Irciniidae Eukaryota n.a. Australian n.a. PMID[20346682]

☑ 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
NPT4641 Individual Protein Glycine receptor subunit alpha-3 Homo sapiens IC50 = 30000.0 nM PMID[534184]

☑ 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 NPC17143 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 NPC47230
0.8235 Intermediate Similarity NPC474431
0.8235 Intermediate Similarity NPC474411
0.8137 Intermediate Similarity NPC469603
0.8077 Intermediate Similarity NPC469597
0.7647 Intermediate Similarity NPC469604
0.7596 Intermediate Similarity NPC474099
0.7573 Intermediate Similarity NPC476926
0.7447 Intermediate Similarity NPC322672
0.7429 Intermediate Similarity NPC476918
0.7426 Intermediate Similarity NPC26597
0.7426 Intermediate Similarity NPC477964
0.7391 Intermediate Similarity NPC473810
0.7368 Intermediate Similarity NPC473525
0.7353 Intermediate Similarity NPC77703
0.734 Intermediate Similarity NPC319913
0.7212 Intermediate Similarity NPC474827
0.7212 Intermediate Similarity NPC199831
0.7212 Intermediate Similarity NPC68001
0.7212 Intermediate Similarity NPC474828
0.7143 Intermediate Similarity NPC476921
0.7115 Intermediate Similarity NPC474244
0.703 Intermediate Similarity NPC150041
0.7011 Intermediate Similarity NPC90782
0.6944 Remote Similarity NPC476276
0.6916 Remote Similarity NPC476328
0.6893 Remote Similarity NPC476344
0.6864 Remote Similarity NPC309525
0.6857 Remote Similarity NPC188785
0.6848 Remote Similarity NPC46268
0.6837 Remote Similarity NPC324506
0.6789 Remote Similarity NPC207820
0.6731 Remote Similarity NPC52820
0.6607 Remote Similarity NPC58281
0.66 Remote Similarity NPC322966
0.6585 Remote Similarity NPC120335
0.6569 Remote Similarity NPC472264
0.6556 Remote Similarity NPC67183
0.6545 Remote Similarity NPC271562
0.6517 Remote Similarity NPC476614
0.6471 Remote Similarity NPC53240
0.6466 Remote Similarity NPC477121
0.6458 Remote Similarity NPC209232
0.6452 Remote Similarity NPC34672
0.6444 Remote Similarity NPC67608
0.6435 Remote Similarity NPC103391
0.6435 Remote Similarity NPC145501
0.6435 Remote Similarity NPC472536
0.641 Remote Similarity NPC471109
0.6395 Remote Similarity NPC174560
0.6395 Remote Similarity NPC125312
0.6364 Remote Similarity NPC321197
0.6339 Remote Similarity NPC476920
0.6339 Remote Similarity NPC171734
0.6311 Remote Similarity NPC159568
0.6306 Remote Similarity NPC185929
0.6292 Remote Similarity NPC308294
0.6292 Remote Similarity NPC142423
0.6286 Remote Similarity NPC313265
0.625 Remote Similarity NPC192006
0.625 Remote Similarity NPC234767
0.625 Remote Similarity NPC145707
0.6228 Remote Similarity NPC63511
0.6226 Remote Similarity NPC40663
0.6214 Remote Similarity NPC81195
0.6207 Remote Similarity NPC130124
0.6207 Remote Similarity NPC193471
0.6196 Remote Similarity NPC328895
0.6195 Remote Similarity NPC476919
0.6176 Remote Similarity NPC472614
0.6174 Remote Similarity NPC476875
0.6168 Remote Similarity NPC476449
0.6154 Remote Similarity NPC236322
0.6154 Remote Similarity NPC476019
0.6147 Remote Similarity NPC233932
0.6142 Remote Similarity NPC133089
0.6139 Remote Similarity NPC76283
0.6134 Remote Similarity NPC474006
0.6129 Remote Similarity NPC288667
0.6129 Remote Similarity NPC29328
0.6126 Remote Similarity NPC265094
0.6126 Remote Similarity NPC476877
0.6121 Remote Similarity NPC261750
0.6121 Remote Similarity NPC60432
0.6121 Remote Similarity NPC314550
0.6121 Remote Similarity NPC1111
0.6111 Remote Similarity NPC91036
0.61 Remote Similarity NPC97913
0.6087 Remote Similarity NPC469914
0.6082 Remote Similarity NPC74410
0.6082 Remote Similarity NPC198240
0.6078 Remote Similarity NPC469483
0.6071 Remote Similarity NPC205176
0.6063 Remote Similarity NPC165726
0.6063 Remote Similarity NPC213969
0.6061 Remote Similarity NPC277341
0.6061 Remote Similarity NPC226982
0.6061 Remote Similarity NPC278459
0.6055 Remote Similarity NPC234542
0.6053 Remote Similarity NPC24596
0.6042 Remote Similarity NPC180886
0.604 Remote Similarity NPC472864
0.604 Remote Similarity NPC19849
0.604 Remote Similarity NPC472865
0.604 Remote Similarity NPC475975
0.604 Remote Similarity NPC164577
0.6038 Remote Similarity NPC38172
0.6034 Remote Similarity NPC47857
0.6034 Remote Similarity NPC181510
0.6034 Remote Similarity NPC168758
0.6034 Remote Similarity NPC21713
0.6034 Remote Similarity NPC475608
0.6022 Remote Similarity NPC318766
0.6022 Remote Similarity NPC97614
0.6019 Remote Similarity NPC123141
0.6018 Remote Similarity NPC271269
0.6018 Remote Similarity NPC476876
0.6018 Remote Similarity NPC154601
0.6017 Remote Similarity NPC474984
0.6 Remote Similarity NPC201889
0.6 Remote Similarity NPC239357
0.6 Remote Similarity NPC174463
0.6 Remote Similarity NPC470536
0.6 Remote Similarity NPC284656
0.6 Remote Similarity NPC316730
0.6 Remote Similarity NPC473224
0.6 Remote Similarity NPC218602
0.6 Remote Similarity NPC106791
0.5984 Remote Similarity NPC23963
0.5984 Remote Similarity NPC315188
0.5982 Remote Similarity NPC474563
0.598 Remote Similarity NPC65661
0.598 Remote Similarity NPC90476
0.598 Remote Similarity NPC69374
0.5979 Remote Similarity NPC472014
0.5979 Remote Similarity NPC61952
0.5977 Remote Similarity NPC274927
0.5977 Remote Similarity NPC106851
0.5969 Remote Similarity NPC120420
0.5965 Remote Similarity NPC251330
0.5963 Remote Similarity NPC150967
0.5957 Remote Similarity NPC160817
0.5946 Remote Similarity NPC100810
0.5946 Remote Similarity NPC144714
0.5946 Remote Similarity NPC474348
0.5946 Remote Similarity NPC474001
0.5946 Remote Similarity NPC316250
0.5941 Remote Similarity NPC1761
0.5941 Remote Similarity NPC52609
0.5938 Remote Similarity NPC244166
0.5938 Remote Similarity NPC251435
0.5938 Remote Similarity NPC472327
0.5934 Remote Similarity NPC322035
0.5934 Remote Similarity NPC100719
0.5934 Remote Similarity NPC166791
0.5929 Remote Similarity NPC64168
0.5929 Remote Similarity NPC472616
0.5923 Remote Similarity NPC99864
0.5922 Remote Similarity NPC469861
0.5922 Remote Similarity NPC261721
0.5922 Remote Similarity NPC130436
0.5922 Remote Similarity NPC186975
0.5922 Remote Similarity NPC472869
0.5922 Remote Similarity NPC469860
0.5918 Remote Similarity NPC93763
0.5918 Remote Similarity NPC108816
0.5918 Remote Similarity NPC128276
0.5918 Remote Similarity NPC59436
0.5918 Remote Similarity NPC169095
0.5918 Remote Similarity NPC476627
0.5913 Remote Similarity NPC307903
0.5913 Remote Similarity NPC470535
0.5913 Remote Similarity NPC140251
0.5905 Remote Similarity NPC174342
0.5902 Remote Similarity NPC230849
0.5902 Remote Similarity NPC11379
0.59 Remote Similarity NPC90055
0.59 Remote Similarity NPC40228
0.59 Remote Similarity NPC471325
0.59 Remote Similarity NPC477372
0.59 Remote Similarity NPC325031
0.5897 Remote Similarity NPC59249
0.5897 Remote Similarity NPC470534
0.5895 Remote Similarity NPC35656
0.5889 Remote Similarity NPC53642
0.5889 Remote Similarity NPC470325
0.5889 Remote Similarity NPC206660
0.5888 Remote Similarity NPC472613
0.5882 Remote Similarity NPC248758
0.5882 Remote Similarity NPC476814
0.5882 Remote Similarity NPC476813
0.5877 Remote Similarity NPC472615
0.5876 Remote Similarity NPC279537
0.5873 Remote Similarity NPC222466
0.5873 Remote Similarity NPC22746
0.587 Remote Similarity NPC476626
0.5868 Remote Similarity NPC120599
0.5868 Remote Similarity NPC471673
0.5868 Remote Similarity NPC156336
0.5868 Remote Similarity NPC200412

  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 NPC17143 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
0.6937 Remote Similarity NPD1376 Discontinued
0.6392 Remote Similarity NPD857 Phase 3
0.625 Remote Similarity NPD3732 Approved
0.6168 Remote Similarity NPD5349 Clinical (unspecified phase)
0.6161 Remote Similarity NPD7333 Discontinued
0.6154 Remote Similarity NPD2682 Approved
0.6122 Remote Similarity NPD612 Discontinued
0.6071 Remote Similarity NPD4281 Clinical (unspecified phase)
0.6063 Remote Similarity NPD5759 Approved
0.6048 Remote Similarity NPD3072 Approved
0.6048 Remote Similarity NPD3073 Approved
0.6048 Remote Similarity NPD3071 Approved
0.6017 Remote Similarity NPD3598 Phase 3
0.6 Remote Similarity NPD790 Approved
0.6 Remote Similarity NPD4677 Discontinued
0.6 Remote Similarity NPD7641 Discontinued
0.5984 Remote Similarity NPD6909 Approved
0.5984 Remote Similarity NPD6908 Approved
0.5969 Remote Similarity NPD6919 Clinical (unspecified phase)
0.5968 Remote Similarity NPD4761 Approved
0.5968 Remote Similarity NPD4762 Approved
0.5968 Remote Similarity NPD4706 Clinical (unspecified phase)
0.5963 Remote Similarity NPD3714 Approved
0.5963 Remote Similarity NPD3715 Approved
0.5963 Remote Similarity NPD3713 Approved
0.5938 Remote Similarity NPD1452 Discontinued
0.5934 Remote Similarity NPD7331 Phase 2
0.5923 Remote Similarity NPD8415 Approved
0.5902 Remote Similarity NPD7299 Clinical (unspecified phase)
0.5891 Remote Similarity NPD4676 Approved
0.5891 Remote Similarity NPD5263 Approved
0.5888 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5878 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5859 Remote Similarity NPD3608 Clinical (unspecified phase)
0.5854 Remote Similarity NPD7739 Clinical (unspecified phase)
0.5825 Remote Similarity NPD5363 Approved
0.582 Remote Similarity NPD3159 Discontinued
0.5814 Remote Similarity NPD3040 Approved
0.5814 Remote Similarity NPD4177 Approved
0.5814 Remote Similarity NPD4175 Approved
0.5806 Remote Similarity NPD7624 Clinical (unspecified phase)
0.5806 Remote Similarity NPD7623 Phase 3
0.5794 Remote Similarity NPD6699 Clinical (unspecified phase)
0.5794 Remote Similarity NPD3677 Clinical (unspecified phase)
0.5785 Remote Similarity NPD961 Discontinued
0.5769 Remote Similarity NPD4125 Approved
0.5765 Remote Similarity NPD3195 Phase 2
0.5765 Remote Similarity NPD3196 Approved
0.5765 Remote Similarity NPD3194 Approved
0.5765 Remote Similarity NPD4266 Approved
0.5763 Remote Similarity NPD2204 Approved
0.5758 Remote Similarity NPD617 Approved
0.5746 Remote Similarity NPD5725 Approved
0.5746 Remote Similarity NPD6073 Approved
0.5735 Remote Similarity NPD7512 Approved
0.5735 Remote Similarity NPD7511 Approved
0.5714 Remote Similarity NPD6404 Discontinued
0.5686 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5682 Remote Similarity NPD5581 Approved
0.5678 Remote Similarity NPD6420 Discontinued
0.5673 Remote Similarity NPD3723 Clinical (unspecified phase)
0.5672 Remote Similarity NPD8643 Discontinued
0.5669 Remote Similarity NPD2584 Suspended
0.5669 Remote Similarity NPD8273 Phase 1
0.5662 Remote Similarity NPD8384 Approved
0.5659 Remote Similarity NPD2585 Clinical (unspecified phase)
0.5656 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5652 Remote Similarity NPD7341 Phase 2
0.5647 Remote Similarity NPD3172 Approved
0.5645 Remote Similarity NPD2645 Approved
0.5644 Remote Similarity NPD5368 Approved
0.5635 Remote Similarity NPD7122 Discontinued
0.5631 Remote Similarity NPD5362 Discontinued
0.5631 Remote Similarity NPD7154 Phase 3
0.563 Remote Similarity NPD5004 Approved
0.5625 Remote Similarity NPD7746 Phase 1
0.5625 Remote Similarity NPD7747 Phase 1
0.5619 Remote Similarity NPD3176 Clinical (unspecified phase)
0.561 Remote Similarity NPD1773 Discontinued
0.56 Remote Similarity NPD5784 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