Structure

Physi-Chem Properties

Molecular Weight:  184.11
Volume:  199.978
LogP:  1.029
LogD:  -0.576
LogS:  -0.416
# Rotatable Bonds:  6
TPSA:  57.53
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.618
Synthetic Accessibility Score:  3.42
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.667
MDCK Permeability:  2.2007188817951828e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.016
Human Intestinal Absorption (HIA):  0.017
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.016

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.83
Plasma Protein Binding (PPB):  63.06787109375%
Volume Distribution (VD):  0.294
Pgp-substrate:  32.54323959350586%

ADMET: Metabolism

CYP1A2-inhibitor:  0.018
CYP1A2-substrate:  0.106
CYP2C19-inhibitor:  0.019
CYP2C19-substrate:  0.071
CYP2C9-inhibitor:  0.013
CYP2C9-substrate:  0.968
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.321
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.06

ADMET: Excretion

Clearance (CL):  3.08
Half-life (T1/2):  0.844

ADMET: Toxicity

hERG Blockers:  0.031
Human Hepatotoxicity (H-HT):  0.458
Drug-inuced Liver Injury (DILI):  0.008
AMES Toxicity:  0.035
Rat Oral Acute Toxicity:  0.602
Maximum Recommended Daily Dose:  0.946
Skin Sensitization:  0.954
Carcinogencity:  0.65
Eye Corrosion:  0.527
Eye Irritation:  0.968
Respiratory Toxicity:  0.866

Download Data

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

  Natural Product: NPC324224

Natural Product ID:  NPC324224
Common Name*:   Ieodomycin D
IUPAC Name:   (2E,4E,9R)-9-hydroxydeca-2,4-dienoic acid
Synonyms:   Ieodomycin D
Standard InCHIKey:  BUNUAXLBBKVLBE-WMCYJUNYSA-N
Standard InCHI:  InChI=1S/C10H16O3/c1-9(11)7-5-3-2-4-6-8-10(12)13/h2,4,6,8-9,11H,3,5,7H2,1H3,(H,12,13)/b4-2+,8-6+/t9-/m1/s1
SMILES:  CC(CCCC=CC=CC(=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1814288
PubChem CID:   53387507
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0003086] Medium-chain fatty acids

*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
NPO30477 Bacillus sp. Species Bacillidae Eukaryota n.a. n.a. n.a. PMID[19322840]
NPO30477 Bacillus sp. Species Bacillidae Eukaryota n.a. n.a. n.a. PMID[21699149]
NPO30477 Bacillus sp. Species Bacillidae Eukaryota n.a. n.a. n.a. PMID[22133265]
NPO30477 Bacillus sp. Species Bacillidae Eukaryota n.a. n.a. n.a. PMID[8641995]
NPO30477 Bacillus sp. Species Bacillidae Eukaryota n.a. n.a. n.a. PMID[9099230]

☑ 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
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 32.0 ug.mL-1 PMID[503918]
NPT19 Organism Escherichia coli Escherichia coli MIC = 32.0 ug.mL-1 PMID[503918]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae MIC = 256.0 ug.mL-1 PMID[503918]

☑ 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 NPC324224 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 NPC472808
0.8525 High Similarity NPC146811
0.8475 Intermediate Similarity NPC26810
0.8448 Intermediate Similarity NPC318306
0.8393 Intermediate Similarity NPC317899
0.8305 Intermediate Similarity NPC327112
0.8136 Intermediate Similarity NPC322002
0.8125 Intermediate Similarity NPC143396
0.8103 Intermediate Similarity NPC44542
0.8103 Intermediate Similarity NPC472445
0.8065 Intermediate Similarity NPC19769
0.8065 Intermediate Similarity NPC96414
0.8 Intermediate Similarity NPC476037
0.7969 Intermediate Similarity NPC63873
0.7937 Intermediate Similarity NPC201356
0.7895 Intermediate Similarity NPC322461
0.7879 Intermediate Similarity NPC293114
0.7879 Intermediate Similarity NPC316185
0.7846 Intermediate Similarity NPC236208
0.7833 Intermediate Similarity NPC97570
0.7833 Intermediate Similarity NPC322186
0.7833 Intermediate Similarity NPC222852
0.7833 Intermediate Similarity NPC329249
0.7812 Intermediate Similarity NPC122627
0.7778 Intermediate Similarity NPC317881
0.7778 Intermediate Similarity NPC136164
0.7778 Intermediate Similarity NPC323045
0.7778 Intermediate Similarity NPC245947
0.7778 Intermediate Similarity NPC255863
0.7761 Intermediate Similarity NPC329890
0.7761 Intermediate Similarity NPC284006
0.7742 Intermediate Similarity NPC473737
0.7727 Intermediate Similarity NPC476012
0.7705 Intermediate Similarity NPC328311
0.7692 Intermediate Similarity NPC474823
0.7679 Intermediate Similarity NPC71053
0.7679 Intermediate Similarity NPC59408
0.7656 Intermediate Similarity NPC37382
0.7647 Intermediate Similarity NPC315843
0.7627 Intermediate Similarity NPC325977
0.7586 Intermediate Similarity NPC110732
0.7586 Intermediate Similarity NPC474127
0.7581 Intermediate Similarity NPC113293
0.7576 Intermediate Similarity NPC475982
0.7576 Intermediate Similarity NPC475004
0.7538 Intermediate Similarity NPC49863
0.7536 Intermediate Similarity NPC260396
0.75 Intermediate Similarity NPC71755
0.75 Intermediate Similarity NPC291437
0.75 Intermediate Similarity NPC221467
0.75 Intermediate Similarity NPC329914
0.75 Intermediate Similarity NPC328784
0.75 Intermediate Similarity NPC323477
0.746 Intermediate Similarity NPC29697
0.7429 Intermediate Similarity NPC188860
0.7424 Intermediate Similarity NPC238223
0.7391 Intermediate Similarity NPC107654
0.7391 Intermediate Similarity NPC227396
0.7385 Intermediate Similarity NPC276299
0.7385 Intermediate Similarity NPC328653
0.7377 Intermediate Similarity NPC223679
0.7368 Intermediate Similarity NPC43053
0.7353 Intermediate Similarity NPC67076
0.7353 Intermediate Similarity NPC319163
0.7344 Intermediate Similarity NPC470320
0.7324 Intermediate Similarity NPC233071
0.7308 Intermediate Similarity NPC221250
0.7302 Intermediate Similarity NPC66460
0.7302 Intermediate Similarity NPC325929
0.7302 Intermediate Similarity NPC271282
0.7302 Intermediate Similarity NPC475984
0.7288 Intermediate Similarity NPC300121
0.7288 Intermediate Similarity NPC137538
0.7273 Intermediate Similarity NPC132286
0.7258 Intermediate Similarity NPC159650
0.7258 Intermediate Similarity NPC329550
0.7258 Intermediate Similarity NPC302564
0.7258 Intermediate Similarity NPC22897
0.7231 Intermediate Similarity NPC282760
0.7231 Intermediate Similarity NPC318420
0.7231 Intermediate Similarity NPC326268
0.7231 Intermediate Similarity NPC320642
0.7222 Intermediate Similarity NPC304079
0.7222 Intermediate Similarity NPC6963
0.7213 Intermediate Similarity NPC323436
0.7213 Intermediate Similarity NPC135863
0.7213 Intermediate Similarity NPC268185
0.7213 Intermediate Similarity NPC129150
0.7213 Intermediate Similarity NPC265551
0.7213 Intermediate Similarity NPC212730
0.7193 Intermediate Similarity NPC20934
0.7193 Intermediate Similarity NPC288381
0.7188 Intermediate Similarity NPC2328
0.7188 Intermediate Similarity NPC470965
0.7167 Intermediate Similarity NPC146551
0.7167 Intermediate Similarity NPC152668
0.7167 Intermediate Similarity NPC471239
0.7167 Intermediate Similarity NPC52264
0.7167 Intermediate Similarity NPC474513
0.7167 Intermediate Similarity NPC470963
0.7143 Intermediate Similarity NPC122521
0.7143 Intermediate Similarity NPC26223
0.7143 Intermediate Similarity NPC174447
0.7143 Intermediate Similarity NPC470686
0.7143 Intermediate Similarity NPC251042
0.7123 Intermediate Similarity NPC1180
0.7119 Intermediate Similarity NPC217188
0.7119 Intermediate Similarity NPC61177
0.7115 Intermediate Similarity NPC8270
0.7101 Intermediate Similarity NPC95863
0.7097 Intermediate Similarity NPC34416
0.7097 Intermediate Similarity NPC254095
0.7097 Intermediate Similarity NPC474084
0.7077 Intermediate Similarity NPC470808
0.7077 Intermediate Similarity NPC226592
0.7069 Intermediate Similarity NPC151782
0.7069 Intermediate Similarity NPC473672
0.7069 Intermediate Similarity NPC474495
0.7059 Intermediate Similarity NPC151481
0.7049 Intermediate Similarity NPC470964
0.7049 Intermediate Similarity NPC327388
0.7049 Intermediate Similarity NPC311648
0.7049 Intermediate Similarity NPC86948
0.7042 Intermediate Similarity NPC478195
0.7042 Intermediate Similarity NPC478196
0.7042 Intermediate Similarity NPC478191
0.7042 Intermediate Similarity NPC478192
0.7042 Intermediate Similarity NPC478193
0.7042 Intermediate Similarity NPC478194
0.7031 Intermediate Similarity NPC55376
0.7031 Intermediate Similarity NPC40082
0.7031 Intermediate Similarity NPC269737
0.7031 Intermediate Similarity NPC477829
0.7018 Intermediate Similarity NPC302310
0.7018 Intermediate Similarity NPC153538
0.7015 Intermediate Similarity NPC25298
0.7015 Intermediate Similarity NPC478097
0.7015 Intermediate Similarity NPC106613
0.7015 Intermediate Similarity NPC26500
0.7015 Intermediate Similarity NPC99619
0.7 Intermediate Similarity NPC189677
0.7 Intermediate Similarity NPC256209
0.7 Intermediate Similarity NPC238948
0.7 Intermediate Similarity NPC12815
0.7 Intermediate Similarity NPC327383
0.7 Intermediate Similarity NPC215745
0.7 Intermediate Similarity NPC185186
0.7 Intermediate Similarity NPC49059
0.7 Intermediate Similarity NPC325627
0.6986 Remote Similarity NPC182292
0.697 Remote Similarity NPC471566
0.697 Remote Similarity NPC478098
0.697 Remote Similarity NPC273600
0.697 Remote Similarity NPC476654
0.697 Remote Similarity NPC182794
0.697 Remote Similarity NPC471565
0.697 Remote Similarity NPC478099
0.697 Remote Similarity NPC476657
0.697 Remote Similarity NPC470123
0.697 Remote Similarity NPC471556
0.697 Remote Similarity NPC476655
0.6964 Remote Similarity NPC308331
0.6957 Remote Similarity NPC59558
0.6957 Remote Similarity NPC473361
0.6957 Remote Similarity NPC329904
0.6949 Remote Similarity NPC35756
0.6944 Remote Similarity NPC326661
0.6935 Remote Similarity NPC594
0.6935 Remote Similarity NPC294938
0.6935 Remote Similarity NPC48968
0.6935 Remote Similarity NPC293437
0.6935 Remote Similarity NPC249850
0.6935 Remote Similarity NPC323597
0.6935 Remote Similarity NPC323498
0.6935 Remote Similarity NPC211752
0.6935 Remote Similarity NPC283502
0.6933 Remote Similarity NPC315731
0.6923 Remote Similarity NPC44343
0.6923 Remote Similarity NPC210303
0.6923 Remote Similarity NPC322457
0.6923 Remote Similarity NPC68110
0.6923 Remote Similarity NPC15934
0.6923 Remote Similarity NPC179087
0.6912 Remote Similarity NPC117804
0.6912 Remote Similarity NPC287705
0.6901 Remote Similarity NPC474321
0.6901 Remote Similarity NPC474545
0.6897 Remote Similarity NPC72699
0.6897 Remote Similarity NPC225974
0.6885 Remote Similarity NPC474913
0.6875 Remote Similarity NPC81896
0.6875 Remote Similarity NPC471278
0.6875 Remote Similarity NPC321919
0.6875 Remote Similarity NPC130953
0.6875 Remote Similarity NPC243532
0.6866 Remote Similarity NPC308294
0.6866 Remote Similarity NPC476656
0.6866 Remote Similarity NPC476659
0.6866 Remote Similarity NPC142423
0.6852 Remote Similarity NPC249801

  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 NPC324224 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
0.8305 Intermediate Similarity NPD4246 Clinical (unspecified phase)
0.7636 Intermediate Similarity NPD4220 Pre-registration
0.7538 Intermediate Similarity NPD4247 Clinical (unspecified phase)
0.6786 Remote Similarity NPD39 Approved
0.6786 Remote Similarity NPD4265 Approved
0.6786 Remote Similarity NPD4222 Approved
0.6724 Remote Similarity NPD3173 Approved
0.6567 Remote Similarity NPD3197 Phase 1
0.6562 Remote Similarity NPD6109 Phase 1
0.6515 Remote Similarity NPD4191 Approved
0.6515 Remote Similarity NPD4194 Approved
0.6515 Remote Similarity NPD4193 Approved
0.6515 Remote Similarity NPD4192 Approved
0.6429 Remote Similarity NPD5326 Phase 3
0.64 Remote Similarity NPD4756 Discovery
0.629 Remote Similarity NPD3172 Approved
0.6271 Remote Similarity NPD5343 Approved
0.6232 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6207 Remote Similarity NPD3174 Discontinued
0.619 Remote Similarity NPD3196 Approved
0.619 Remote Similarity NPD3194 Approved
0.619 Remote Similarity NPD3195 Phase 2
0.619 Remote Similarity NPD4266 Approved
0.6173 Remote Similarity NPD5363 Approved
0.614 Remote Similarity NPD9411 Phase 1
0.6104 Remote Similarity NPD5784 Clinical (unspecified phase)
0.6104 Remote Similarity NPD4271 Approved
0.6104 Remote Similarity NPD4268 Approved
0.6061 Remote Similarity NPD585 Clinical (unspecified phase)
0.6034 Remote Similarity NPD6097 Approved
0.6034 Remote Similarity NPD6096 Approved
0.6029 Remote Similarity NPD368 Approved
0.6 Remote Similarity NPD7838 Discovery
0.5968 Remote Similarity NPD6927 Phase 3
0.5949 Remote Similarity NPD4252 Approved
0.5949 Remote Similarity NPD4820 Approved
0.5949 Remote Similarity NPD4822 Approved
0.5949 Remote Similarity NPD4821 Approved
0.5949 Remote Similarity NPD4819 Approved
0.5949 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5942 Remote Similarity NPD3210 Clinical (unspecified phase)
0.5867 Remote Similarity NPD4732 Discontinued
0.5854 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5846 Remote Similarity NPD342 Phase 1
0.5814 Remote Similarity NPD5785 Approved
0.5802 Remote Similarity NPD5209 Approved
0.5802 Remote Similarity NPD4270 Approved
0.5802 Remote Similarity NPD4269 Approved
0.5758 Remote Similarity NPD4219 Approved
0.5738 Remote Similarity NPD622 Approved
0.5732 Remote Similarity NPD5332 Approved
0.5732 Remote Similarity NPD5331 Approved
0.5732 Remote Similarity NPD7154 Phase 3
0.5732 Remote Similarity NPD5362 Discontinued
0.5714 Remote Similarity NPD29 Approved
0.5714 Remote Similarity NPD28 Approved
0.5714 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5714 Remote Similarity NPD8264 Approved
0.5679 Remote Similarity NPD4790 Discontinued
0.566 Remote Similarity NPD8573 Approved
0.5634 Remote Similarity NPD5325 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