Structure

Physi-Chem Properties

Molecular Weight:  292.2
Volume:  327.153
LogP:  5.898
LogD:  4.593
LogS:  -4.692
# Rotatable Bonds:  8
TPSA:  50.44
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.559
Synthetic Accessibility Score:  2.875
Fsp3:  0.611
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:  -4.652
MDCK Permeability:  2.4794713681330904e-05
Pgp-inhibitor:  0.572
Pgp-substrate:  0.015
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.938
30% Bioavailability (F30%):  0.239

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.147
Plasma Protein Binding (PPB):  98.8365249633789%
Volume Distribution (VD):  3.829
Pgp-substrate:  2.0503642559051514%

ADMET: Metabolism

CYP1A2-inhibitor:  0.902
CYP1A2-substrate:  0.638
CYP2C19-inhibitor:  0.872
CYP2C19-substrate:  0.555
CYP2C9-inhibitor:  0.868
CYP2C9-substrate:  0.965
CYP2D6-inhibitor:  0.167
CYP2D6-substrate:  0.679
CYP3A4-inhibitor:  0.358
CYP3A4-substrate:  0.097

ADMET: Excretion

Clearance (CL):  3.637
Half-life (T1/2):  0.252

ADMET: Toxicity

hERG Blockers:  0.007
Human Hepatotoxicity (H-HT):  0.957
Drug-inuced Liver Injury (DILI):  0.854
AMES Toxicity:  0.015
Rat Oral Acute Toxicity:  0.172
Maximum Recommended Daily Dose:  0.028
Skin Sensitization:  0.611
Carcinogencity:  0.269
Eye Corrosion:  0.004
Eye Irritation:  0.048
Respiratory Toxicity:  0.153

Download Data

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

  Natural Product: NPC471556

Natural Product ID:  NPC471556
Common Name*:   Iromycin Mo
IUPAC Name:   4-hydroxy-3-methyl-6-[(E)-3-methyloct-2-enyl]-5-propylpyran-2-one
Synonyms:   iromycin MO
Standard InCHIKey:  MIXQIMNQZANDMA-ACCUITESSA-N
Standard InCHI:  InChI=1S/C18H28O3/c1-5-7-8-10-13(3)11-12-16-15(9-6-2)17(19)14(4)18(20)21-16/h11,19H,5-10,12H2,1-4H3/b13-11+
SMILES:  CCCCC/C(=C/Cc1oc(=O)c(c(c1CCC)O)C)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL256862
PubChem CID:   54732498
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000086] Pyrans
        • [CHEMONTID:0000481] Pyranones and derivatives

*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
NPO33217 streptomyces sp. dra 17 Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[18054490]

☑ 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
NPT5098 Protein Complex Mitochondrial complex I; NADH oxidoreductase Bos taurus IC50 = 8550.0 nM PMID[546228]

☑ 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 NPC471556 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
0.9355 High Similarity NPC471566
0.9355 High Similarity NPC471565
0.8657 High Similarity NPC315597
0.8636 High Similarity NPC313444
0.8615 High Similarity NPC315115
0.8485 Intermediate Similarity NPC132286
0.8382 Intermediate Similarity NPC316029
0.8382 Intermediate Similarity NPC315285
0.8358 Intermediate Similarity NPC238223
0.8333 Intermediate Similarity NPC218486
0.8116 Intermediate Similarity NPC59558
0.7969 Intermediate Similarity NPC133600
0.7945 Intermediate Similarity NPC315394
0.7903 Intermediate Similarity NPC173157
0.7879 Intermediate Similarity NPC2328
0.7826 Intermediate Similarity NPC79220
0.7826 Intermediate Similarity NPC474823
0.7778 Intermediate Similarity NPC86948
0.7714 Intermediate Similarity NPC475004
0.7714 Intermediate Similarity NPC151481
0.7714 Intermediate Similarity NPC473277
0.7705 Intermediate Similarity NPC191643
0.7703 Intermediate Similarity NPC316324
0.7647 Intermediate Similarity NPC182794
0.7619 Intermediate Similarity NPC478117
0.7576 Intermediate Similarity NPC429928
0.7538 Intermediate Similarity NPC189700
0.7536 Intermediate Similarity NPC146811
0.7536 Intermediate Similarity NPC191233
0.7536 Intermediate Similarity NPC37382
0.7534 Intermediate Similarity NPC470686
0.75 Intermediate Similarity NPC234084
0.75 Intermediate Similarity NPC316185
0.75 Intermediate Similarity NPC221763
0.75 Intermediate Similarity NPC126184
0.7463 Intermediate Similarity NPC15193
0.746 Intermediate Similarity NPC478120
0.7432 Intermediate Similarity NPC478193
0.7432 Intermediate Similarity NPC478192
0.7432 Intermediate Similarity NPC478195
0.7432 Intermediate Similarity NPC478196
0.7432 Intermediate Similarity NPC478194
0.7432 Intermediate Similarity NPC478191
0.7391 Intermediate Similarity NPC96414
0.7391 Intermediate Similarity NPC282760
0.7391 Intermediate Similarity NPC220766
0.7385 Intermediate Similarity NPC249850
0.7385 Intermediate Similarity NPC135863
0.7385 Intermediate Similarity NPC293437
0.7368 Intermediate Similarity NPC315765
0.7361 Intermediate Similarity NPC476037
0.7361 Intermediate Similarity NPC329904
0.7361 Intermediate Similarity NPC473361
0.7353 Intermediate Similarity NPC44343
0.7353 Intermediate Similarity NPC210303
0.7353 Intermediate Similarity NPC68110
0.7353 Intermediate Similarity NPC179087
0.7353 Intermediate Similarity NPC473737
0.7324 Intermediate Similarity NPC287705
0.7313 Intermediate Similarity NPC130953
0.7297 Intermediate Similarity NPC315843
0.7286 Intermediate Similarity NPC201356
0.7286 Intermediate Similarity NPC470033
0.7273 Intermediate Similarity NPC254095
0.7273 Intermediate Similarity NPC474084
0.726 Intermediate Similarity NPC293114
0.7246 Intermediate Similarity NPC475618
0.7246 Intermediate Similarity NPC477457
0.7246 Intermediate Similarity NPC477456
0.7231 Intermediate Similarity NPC51846
0.7231 Intermediate Similarity NPC150717
0.7222 Intermediate Similarity NPC470693
0.7222 Intermediate Similarity NPC232812
0.7206 Intermediate Similarity NPC26810
0.72 Intermediate Similarity NPC315552
0.72 Intermediate Similarity NPC260396
0.7183 Intermediate Similarity NPC21998
0.7164 Intermediate Similarity NPC159650
0.7164 Intermediate Similarity NPC222852
0.7164 Intermediate Similarity NPC22897
0.7164 Intermediate Similarity NPC286189
0.7162 Intermediate Similarity NPC329890
0.7162 Intermediate Similarity NPC284006
0.7162 Intermediate Similarity NPC316851
0.716 Intermediate Similarity NPC67081
0.716 Intermediate Similarity NPC471223
0.7143 Intermediate Similarity NPC273600
0.7143 Intermediate Similarity NPC7940
0.7125 Intermediate Similarity NPC475083
0.7125 Intermediate Similarity NPC16488
0.7123 Intermediate Similarity NPC37929
0.7123 Intermediate Similarity NPC476012
0.7123 Intermediate Similarity NPC64234
0.7123 Intermediate Similarity NPC202011
0.7121 Intermediate Similarity NPC283502
0.7108 Intermediate Similarity NPC473658
0.7105 Intermediate Similarity NPC301207
0.7105 Intermediate Similarity NPC470705
0.7101 Intermediate Similarity NPC132243
0.7101 Intermediate Similarity NPC155849
0.7101 Intermediate Similarity NPC475073
0.7083 Intermediate Similarity NPC477117
0.7077 Intermediate Similarity NPC25038
0.7073 Intermediate Similarity NPC315395
0.7073 Intermediate Similarity NPC316426
0.7067 Intermediate Similarity NPC107654
0.7059 Intermediate Similarity NPC79756
0.7059 Intermediate Similarity NPC26223
0.7059 Intermediate Similarity NPC309408
0.7059 Intermediate Similarity NPC98519
0.7051 Intermediate Similarity NPC271632
0.7049 Intermediate Similarity NPC128520
0.7042 Intermediate Similarity NPC142423
0.7042 Intermediate Similarity NPC248125
0.7042 Intermediate Similarity NPC308294
0.7037 Intermediate Similarity NPC475706
0.7027 Intermediate Similarity NPC181587
0.7027 Intermediate Similarity NPC133098
0.7027 Intermediate Similarity NPC178575
0.7024 Intermediate Similarity NPC307092
0.7015 Intermediate Similarity NPC21946
0.7015 Intermediate Similarity NPC223679
0.7013 Intermediate Similarity NPC262747
0.7013 Intermediate Similarity NPC471225
0.7013 Intermediate Similarity NPC475711
0.7013 Intermediate Similarity NPC176329
0.7013 Intermediate Similarity NPC51809
0.7013 Intermediate Similarity NPC474818
0.7013 Intermediate Similarity NPC125365
0.7013 Intermediate Similarity NPC49302
0.7 Intermediate Similarity NPC474028
0.7 Intermediate Similarity NPC474439
0.6986 Remote Similarity NPC236208
0.6984 Remote Similarity NPC43053
0.6977 Remote Similarity NPC282644
0.6977 Remote Similarity NPC29798
0.697 Remote Similarity NPC472808
0.697 Remote Similarity NPC325977
0.697 Remote Similarity NPC324224
0.6962 Remote Similarity NPC160582
0.6957 Remote Similarity NPC151648
0.6951 Remote Similarity NPC307112
0.6944 Remote Similarity NPC203335
0.6944 Remote Similarity NPC122627
0.6944 Remote Similarity NPC225272
0.6933 Remote Similarity NPC185186
0.6933 Remote Similarity NPC327383
0.6933 Remote Similarity NPC12815
0.6933 Remote Similarity NPC238948
0.6933 Remote Similarity NPC215745
0.6933 Remote Similarity NPC329914
0.6923 Remote Similarity NPC221095
0.6923 Remote Similarity NPC209135
0.6923 Remote Similarity NPC322461
0.6923 Remote Similarity NPC473471
0.6923 Remote Similarity NPC108816
0.6923 Remote Similarity NPC474816
0.6923 Remote Similarity NPC279214
0.6923 Remote Similarity NPC474127
0.6923 Remote Similarity NPC93763
0.6914 Remote Similarity NPC475714
0.6914 Remote Similarity NPC44261
0.6912 Remote Similarity NPC82465
0.6905 Remote Similarity NPC26078
0.6905 Remote Similarity NPC260343
0.6901 Remote Similarity NPC133904
0.6901 Remote Similarity NPC470688
0.6901 Remote Similarity NPC470123
0.6901 Remote Similarity NPC476589
0.6901 Remote Similarity NPC19769
0.6892 Remote Similarity NPC67183
0.6892 Remote Similarity NPC4299
0.6885 Remote Similarity NPC128280
0.6885 Remote Similarity NPC308331
0.6883 Remote Similarity NPC188860
0.6883 Remote Similarity NPC127118
0.6883 Remote Similarity NPC209113
0.6867 Remote Similarity NPC47220
0.6867 Remote Similarity NPC186332
0.6866 Remote Similarity NPC129150
0.6866 Remote Similarity NPC44542
0.6866 Remote Similarity NPC294938
0.686 Remote Similarity NPC32552
0.6857 Remote Similarity NPC217940
0.6849 Remote Similarity NPC310210
0.6849 Remote Similarity NPC63873
0.6849 Remote Similarity NPC470256
0.6835 Remote Similarity NPC469617
0.6833 Remote Similarity NPC6963
0.6833 Remote Similarity NPC304079
0.6829 Remote Similarity NPC196487
0.6829 Remote Similarity NPC14575
0.6825 Remote Similarity NPC221467
0.6825 Remote Similarity NPC236338
0.6824 Remote Similarity NPC51358
0.6812 Remote Similarity NPC476585
0.6812 Remote Similarity NPC327112
0.6806 Remote Similarity NPC475555
0.6806 Remote Similarity NPC469446
0.6806 Remote Similarity NPC475675

  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 NPC471556 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
0.7467 Intermediate Similarity NPD4756 Discovery
0.7213 Intermediate Similarity NPD4220 Pre-registration
0.6812 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6719 Remote Similarity NPD6927 Phase 3
0.6714 Remote Similarity NPD4194 Approved
0.6714 Remote Similarity NPD4193 Approved
0.6714 Remote Similarity NPD4191 Approved
0.6714 Remote Similarity NPD4192 Approved
0.6667 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6627 Remote Similarity NPD6400 Clinical (unspecified phase)
0.6301 Remote Similarity NPD5325 Clinical (unspecified phase)
0.6267 Remote Similarity NPD4247 Clinical (unspecified phase)
0.619 Remote Similarity NPD39 Approved
0.619 Remote Similarity NPD4222 Approved
0.618 Remote Similarity NPD7838 Discovery
0.6164 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6154 Remote Similarity NPD3173 Approved
0.6143 Remote Similarity NPD8779 Phase 3
0.6129 Remote Similarity NPD9411 Phase 1
0.6125 Remote Similarity NPD8039 Approved
0.6118 Remote Similarity NPD7154 Phase 3
0.6064 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6029 Remote Similarity NPD3172 Approved
0.6 Remote Similarity NPD6698 Approved
0.6 Remote Similarity NPD5209 Approved
0.6 Remote Similarity NPD46 Approved
0.5942 Remote Similarity NPD3196 Approved
0.5942 Remote Similarity NPD4266 Approved
0.5942 Remote Similarity NPD3194 Approved
0.5942 Remote Similarity NPD3195 Phase 2
0.5938 Remote Similarity NPD4265 Approved
0.5921 Remote Similarity NPD3704 Approved
0.5921 Remote Similarity NPD6108 Clinical (unspecified phase)
0.5918 Remote Similarity NPD5909 Discontinued
0.5873 Remote Similarity NPD5326 Phase 3
0.5843 Remote Similarity NPD1282 Approved
0.5833 Remote Similarity NPD6109 Phase 1
0.5765 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5761 Remote Similarity NPD7637 Suspended
0.5758 Remote Similarity NPD5343 Approved
0.573 Remote Similarity NPD4249 Approved
0.5729 Remote Similarity NPD4225 Approved
0.5714 Remote Similarity NPD7331 Phase 2
0.5699 Remote Similarity NPD5779 Approved
0.5699 Remote Similarity NPD5778 Approved
0.5692 Remote Similarity NPD3174 Discontinued
0.567 Remote Similarity NPD6648 Approved
0.5667 Remote Similarity NPD4250 Approved
0.5667 Remote Similarity NPD4251 Approved
0.5652 Remote Similarity NPD5785 Approved
0.5632 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5618 Remote Similarity NPD6082 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