Structure

Physi-Chem Properties

Molecular Weight:  471.26
Volume:  501.082
LogP:  4.319
LogD:  3.658
LogS:  -3.777
# Rotatable Bonds:  13
TPSA:  116.06
# H-Bond Aceptor:  7
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.249
Synthetic Accessibility Score:  3.693
Fsp3:  0.444
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:  -5.54
MDCK Permeability:  2.1160933101782575e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.497
Human Intestinal Absorption (HIA):  0.86
20% Bioavailability (F20%):  0.026
30% Bioavailability (F30%):  0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.002
Plasma Protein Binding (PPB):  97.12606048583984%
Volume Distribution (VD):  0.176
Pgp-substrate:  0.6838876605033875%

ADMET: Metabolism

CYP1A2-inhibitor:  0.283
CYP1A2-substrate:  0.242
CYP2C19-inhibitor:  0.08
CYP2C19-substrate:  0.054
CYP2C9-inhibitor:  0.822
CYP2C9-substrate:  0.987
CYP2D6-inhibitor:  0.618
CYP2D6-substrate:  0.809
CYP3A4-inhibitor:  0.053
CYP3A4-substrate:  0.074

ADMET: Excretion

Clearance (CL):  1.884
Half-life (T1/2):  0.92

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.892
Drug-inuced Liver Injury (DILI):  0.974
AMES Toxicity:  0.001
Rat Oral Acute Toxicity:  0.042
Maximum Recommended Daily Dose:  0.552
Skin Sensitization:  0.857
Carcinogencity:  0.037
Eye Corrosion:  0.003
Eye Irritation:  0.099
Respiratory Toxicity:  0.05

Download Data

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

  Natural Product: NPC26597

Natural Product ID:  NPC26597
Common Name*:   Ircinialactam A
IUPAC Name:   2-[4-[(3E,7E,12S,13Z)-13-(3-hydroxy-4-methyl-5-oxofuran-2-ylidene)-4,8,12-trimethyltrideca-3,7-dienyl]-5-oxo-2H-pyrrol-1-yl]acetic acid
Synonyms:  
Standard InCHIKey:  BIQICBSXLAWWPY-CHVWLSOJSA-N
Standard InCHI:  InChI=1S/C27H37NO6/c1-18(10-6-12-20(3)16-23-25(31)21(4)27(33)34-23)8-5-9-19(2)11-7-13-22-14-15-28(26(22)32)17-24(29)30/h8,11,14,16,20,31H,5-7,9-10,12-13,15,17H2,1-4H3,(H,29,30)/b18-8+,19-11+,23-16-/t20-/m0/s1
SMILES:  C/C(=CCC/C(=C/CCC1=CCN(C1=O)CC(=O)O)/C)/CCC[C@@H](/C=C/1OC(=O)C(=C1O)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1093582
PubChem CID:   54726844
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones
          • [CHEMONTID:0001538] Diterpene lactones

*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
NPT426 Individual Protein Glycine receptor subunit alpha-1 Homo sapiens Activity = 140.0 % PMID[492462]
NPT4641 Individual Protein Glycine receptor subunit alpha-3 Homo sapiens IC50 = 30000.0 nM PMID[492462]

☑ 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 NPC26597 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
0.9109 High Similarity NPC469603
0.899 High Similarity NPC469604
0.8725 High Similarity NPC474099
0.86 High Similarity NPC474244
0.8333 Intermediate Similarity NPC474827
0.8333 Intermediate Similarity NPC199831
0.8333 Intermediate Similarity NPC474828
0.8333 Intermediate Similarity NPC68001
0.82 Intermediate Similarity NPC52820
0.7426 Intermediate Similarity NPC17143
0.7426 Intermediate Similarity NPC47230
0.7043 Intermediate Similarity NPC469597
0.7018 Intermediate Similarity NPC474411
0.7018 Intermediate Similarity NPC474431
0.6931 Remote Similarity NPC474424
0.6838 Remote Similarity NPC103391
0.6838 Remote Similarity NPC472536
0.6699 Remote Similarity NPC469861
0.6699 Remote Similarity NPC130436
0.6699 Remote Similarity NPC469860
0.6693 Remote Similarity NPC213969
0.6693 Remote Similarity NPC165726
0.6667 Remote Similarity NPC188785
0.6634 Remote Similarity NPC474439
0.6634 Remote Similarity NPC474028
0.6581 Remote Similarity NPC47857
0.6581 Remote Similarity NPC181510
0.6581 Remote Similarity NPC168758
0.6579 Remote Similarity NPC476926
0.6571 Remote Similarity NPC475739
0.6562 Remote Similarity NPC120335
0.6514 Remote Similarity NPC150041
0.6471 Remote Similarity NPC130124
0.6471 Remote Similarity NPC193471
0.6466 Remote Similarity NPC476918
0.6422 Remote Similarity NPC313265
0.6408 Remote Similarity NPC475714
0.6396 Remote Similarity NPC476344
0.6392 Remote Similarity NPC252503
0.6389 Remote Similarity NPC472264
0.6348 Remote Similarity NPC476921
0.6348 Remote Similarity NPC64168
0.6346 Remote Similarity NPC475706
0.6261 Remote Similarity NPC279833
0.6261 Remote Similarity NPC6271
0.6261 Remote Similarity NPC173690
0.6261 Remote Similarity NPC80439
0.626 Remote Similarity NPC106791
0.626 Remote Similarity NPC284656
0.626 Remote Similarity NPC201889
0.625 Remote Similarity NPC90782
0.6204 Remote Similarity NPC81195
0.6167 Remote Similarity NPC58281
0.6167 Remote Similarity NPC30911
0.6167 Remote Similarity NPC316984
0.616 Remote Similarity NPC11379
0.6147 Remote Similarity NPC474098
0.6147 Remote Similarity NPC475995
0.614 Remote Similarity NPC474985
0.6132 Remote Similarity NPC319913
0.6106 Remote Similarity NPC150967
0.6102 Remote Similarity NPC271562
0.6094 Remote Similarity NPC469999
0.6087 Remote Similarity NPC77703
0.6075 Remote Similarity NPC322672
0.6071 Remote Similarity NPC469739
0.6068 Remote Similarity NPC205176
0.6061 Remote Similarity NPC326126
0.6058 Remote Similarity NPC277341
0.6058 Remote Similarity NPC226982
0.6038 Remote Similarity NPC475975
0.6019 Remote Similarity NPC473525
0.6018 Remote Similarity NPC175614
0.6017 Remote Similarity NPC476328
0.6 Remote Similarity NPC159568
0.6 Remote Similarity NPC473810
0.6 Remote Similarity NPC235625
0.5985 Remote Similarity NPC477988
0.5984 Remote Similarity NPC314550
0.5984 Remote Similarity NPC23963
0.5946 Remote Similarity NPC72183
0.5946 Remote Similarity NPC299808
0.5946 Remote Similarity NPC118844
0.5946 Remote Similarity NPC110875
0.592 Remote Similarity NPC65045
0.592 Remote Similarity NPC475642
0.5917 Remote Similarity NPC476276
0.5917 Remote Similarity NPC470072
0.5906 Remote Similarity NPC477140
0.5906 Remote Similarity NPC477143
0.5872 Remote Similarity NPC45409
0.5856 Remote Similarity NPC53240
0.5854 Remote Similarity NPC43648
0.5854 Remote Similarity NPC474497
0.585 Remote Similarity NPC475342
0.5846 Remote Similarity NPC321197
0.5842 Remote Similarity NPC470686
0.5825 Remote Similarity NPC316324
0.5825 Remote Similarity NPC68156
0.582 Remote Similarity NPC195435
0.582 Remote Similarity NPC196073
0.5816 Remote Similarity NPC313444
0.5816 Remote Similarity NPC96272
0.5802 Remote Similarity NPC329401
0.5802 Remote Similarity NPC477987
0.5802 Remote Similarity NPC309525
0.5789 Remote Similarity NPC155849
0.5784 Remote Similarity NPC478191
0.5784 Remote Similarity NPC478193
0.5784 Remote Similarity NPC478192
0.5784 Remote Similarity NPC478194
0.5784 Remote Similarity NPC478195
0.5784 Remote Similarity NPC478196
0.5781 Remote Similarity NPC230849
0.5778 Remote Similarity NPC133089
0.5764 Remote Similarity NPC135121
0.5763 Remote Similarity NPC473289
0.576 Remote Similarity NPC474984
0.5758 Remote Similarity NPC470693
0.5752 Remote Similarity NPC38172
0.575 Remote Similarity NPC271269
0.575 Remote Similarity NPC154601
0.5748 Remote Similarity NPC200412
0.5748 Remote Similarity NPC156336
0.5748 Remote Similarity NPC120599
0.5741 Remote Similarity NPC161670
0.5736 Remote Similarity NPC475383
0.5736 Remote Similarity NPC156379
0.5736 Remote Similarity NPC470000
0.5735 Remote Similarity NPC120420
0.5734 Remote Similarity NPC477217
0.5734 Remote Similarity NPC201244
0.5726 Remote Similarity NPC275100
0.5726 Remote Similarity NPC477964
0.5725 Remote Similarity NPC36254
0.5714 Remote Similarity NPC473056
0.5714 Remote Similarity NPC315848
0.5714 Remote Similarity NPC471768
0.5714 Remote Similarity NPC315210
0.5702 Remote Similarity NPC251330
0.5701 Remote Similarity NPC16321
0.57 Remote Similarity NPC315597
0.57 Remote Similarity NPC37929
0.57 Remote Similarity NPC64234
0.57 Remote Similarity NPC316029
0.57 Remote Similarity NPC473361
0.57 Remote Similarity NPC67183
0.57 Remote Similarity NPC329904
0.5693 Remote Similarity NPC99864
0.5691 Remote Similarity NPC113012
0.5691 Remote Similarity NPC122926
0.569 Remote Similarity NPC241426
0.569 Remote Similarity NPC265662
0.5688 Remote Similarity NPC296589
0.5686 Remote Similarity NPC474758
0.5686 Remote Similarity NPC315843
0.5686 Remote Similarity NPC107654
0.5678 Remote Similarity NPC175531
0.5676 Remote Similarity NPC155230
0.5673 Remote Similarity NPC46268
0.567 Remote Similarity NPC213560
0.5669 Remote Similarity NPC469997
0.5652 Remote Similarity NPC189764
0.5652 Remote Similarity NPC50902
0.5652 Remote Similarity NPC233273
0.5652 Remote Similarity NPC205546
0.5649 Remote Similarity NPC477990
0.5649 Remote Similarity NPC111162
0.5649 Remote Similarity NPC323168
0.5649 Remote Similarity NPC293550
0.5649 Remote Similarity NPC477989
0.5648 Remote Similarity NPC475947
0.5645 Remote Similarity NPC21713
0.5645 Remote Similarity NPC475608
0.5639 Remote Similarity NPC473249
0.5636 Remote Similarity NPC469483
0.5631 Remote Similarity NPC329852
0.563 Remote Similarity NPC307165
0.5625 Remote Similarity NPC174463
0.5619 Remote Similarity NPC315765
0.5614 Remote Similarity NPC282644
0.5614 Remote Similarity NPC304897
0.5614 Remote Similarity NPC29798
0.5614 Remote Similarity NPC247316
0.5612 Remote Similarity NPC191233
0.5612 Remote Similarity NPC315115
0.561 Remote Similarity NPC24389
0.5607 Remote Similarity NPC284456
0.56 Remote Similarity NPC232812
0.56 Remote Similarity NPC474995

  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 NPC26597 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 NPD1376 Discontinued
0.6167 Remote Similarity NPD2204 Approved
0.61 Remote Similarity NPD1452 Discontinued
0.6032 Remote Similarity NPD7299 Clinical (unspecified phase)
0.5952 Remote Similarity NPD2495 Phase 3
0.5814 Remote Similarity NPD7623 Phase 3
0.5814 Remote Similarity NPD7624 Clinical (unspecified phase)
0.5802 Remote Similarity NPD8273 Phase 1
0.5766 Remote Similarity NPD8387 Clinical (unspecified phase)
0.575 Remote Similarity NPD777 Phase 3
0.5736 Remote Similarity NPD7739 Clinical (unspecified phase)
0.5693 Remote Similarity NPD8415 Approved
0.5639 Remote Similarity NPD7746 Phase 1
0.5639 Remote Similarity NPD7747 Phase 1
0.5625 Remote Similarity NPD1773 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