Structure

Physi-Chem Properties

Molecular Weight:  421.26
Volume:  477.994
LogP:  0.451
LogD:  1.592
LogS:  -4.116
# Rotatable Bonds:  3
TPSA:  69.56
# H-Bond Aceptor:  4
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.574
Synthetic Accessibility Score:  5.258
Fsp3:  0.296
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:  -5.071
MDCK Permeability:  1.9797478671534918e-05
Pgp-inhibitor:  0.006
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.068
20% Bioavailability (F20%):  0.407
30% Bioavailability (F30%):  0.072

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.006
Plasma Protein Binding (PPB):  91.65152740478516%
Volume Distribution (VD):  0.542
Pgp-substrate:  4.983421802520752%

ADMET: Metabolism

CYP1A2-inhibitor:  0.617
CYP1A2-substrate:  0.126
CYP2C19-inhibitor:  0.502
CYP2C19-substrate:  0.106
CYP2C9-inhibitor:  0.656
CYP2C9-substrate:  0.999
CYP2D6-inhibitor:  0.877
CYP2D6-substrate:  0.947
CYP3A4-inhibitor:  0.828
CYP3A4-substrate:  0.044

ADMET: Excretion

Clearance (CL):  0.815
Half-life (T1/2):  0.241

ADMET: Toxicity

hERG Blockers:  0.275
Human Hepatotoxicity (H-HT):  0.886
Drug-inuced Liver Injury (DILI):  0.525
AMES Toxicity:  0.544
Rat Oral Acute Toxicity:  0.024
Maximum Recommended Daily Dose:  0.98
Skin Sensitization:  0.932
Carcinogencity:  0.781
Eye Corrosion:  0.004
Eye Irritation:  0.05
Respiratory Toxicity:  0.892

Download Data

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

  Natural Product: NPC129995

Natural Product ID:  NPC129995
Common Name*:   Heronamide F
IUPAC Name:   (3E,5E,7E,9S,10R,11Z,13E,15E,17E,20R)-20-[(2E,4E)-hexa-2,4-dienyl]-9,10-dihydroxy-7,15-dimethyl-1-azacycloicosa-3,5,7,11,13,15,17-heptaen-2-one
Synonyms:  
Standard InCHIKey:  FFBLFSFSCNGUGS-YGXGVOTQSA-N
Standard InCHI:  InChI=1S/C27H35NO3/c1-4-5-6-7-17-24-18-11-8-14-22(2)15-9-12-19-25(29)26(30)21-23(3)16-10-13-20-27(31)28-24/h4-16,19-21,24-26,29-30H,17-18H2,1-3H3,(H,28,31)/b5-4+,7-6+,11-8+,15-9+,16-10+,19-12-,20-13+,22-14+,23-21+/t24-,25-,26+/m1/s1
SMILES:  C/C=C/C=C/C[C@@H]1C/C=C/C=C(C)/C=C/C=C[C@H]([C@H](/C=C(C)/C=C/C=C/C(=N1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3109452
PubChem CID:   76310274
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000064] Macrolactams

*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
NPO40641 Streptomyces sp. SCSIO 03032 Strain Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[24547685]
NPO40641 Streptomyces sp. SCSIO 03032 Strain Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[25069084]

☑ 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
NPT397 Cell Line NCI-H460 Homo sapiens IC50 > 100000.0 nM PMID[496694]
NPT395 Cell Line SF-268 Homo sapiens IC50 > 100000.0 nM PMID[496694]
NPT83 Cell Line MCF7 Homo sapiens IC50 > 100000.0 nM PMID[496694]
NPT20 Organism Candida albicans Candida albicans MIC > 128.0 ug.mL-1 PMID[496694]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC > 128.0 ug.mL-1 PMID[496694]
NPT1261 Organism Bacillus thuringiensis Bacillus thuringiensis MIC > 128.0 ug.mL-1 PMID[496694]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 128.0 ug.mL-1 PMID[496694]
NPT19 Organism Escherichia coli Escherichia coli MIC > 128.0 ug.mL-1 PMID[496694]

☑ 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 NPC129995 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 NPC315141
0.9104 High Similarity NPC314678
0.875 High Similarity NPC253468
0.875 High Similarity NPC235311
0.8615 High Similarity NPC477525
0.8308 Intermediate Similarity NPC471023
0.7879 Intermediate Similarity NPC29468
0.7727 Intermediate Similarity NPC130807
0.7619 Intermediate Similarity NPC246519
0.7619 Intermediate Similarity NPC132669
0.7619 Intermediate Similarity NPC184014
0.7619 Intermediate Similarity NPC44193
0.7619 Intermediate Similarity NPC14234
0.7619 Intermediate Similarity NPC269800
0.7606 Intermediate Similarity NPC471022
0.7576 Intermediate Similarity NPC312826
0.75 Intermediate Similarity NPC297020
0.75 Intermediate Similarity NPC471992
0.746 Intermediate Similarity NPC303672
0.7432 Intermediate Similarity NPC288086
0.7419 Intermediate Similarity NPC145032
0.7419 Intermediate Similarity NPC267340
0.7419 Intermediate Similarity NPC243539
0.7419 Intermediate Similarity NPC54542
0.7419 Intermediate Similarity NPC304223
0.7385 Intermediate Similarity NPC261158
0.7385 Intermediate Similarity NPC24216
0.7385 Intermediate Similarity NPC104138
0.7385 Intermediate Similarity NPC306420
0.7361 Intermediate Similarity NPC291196
0.7361 Intermediate Similarity NPC103712
0.7313 Intermediate Similarity NPC150505
0.7313 Intermediate Similarity NPC74617
0.7302 Intermediate Similarity NPC195986
0.7258 Intermediate Similarity NPC307435
0.7258 Intermediate Similarity NPC267692
0.7231 Intermediate Similarity NPC471991
0.7231 Intermediate Similarity NPC273023
0.7229 Intermediate Similarity NPC316186
0.7206 Intermediate Similarity NPC6795
0.7188 Intermediate Similarity NPC119655
0.7077 Intermediate Similarity NPC163912
0.7077 Intermediate Similarity NPC305288
0.7077 Intermediate Similarity NPC167759
0.7077 Intermediate Similarity NPC56028
0.697 Remote Similarity NPC242930
0.6892 Remote Similarity NPC45060
0.6892 Remote Similarity NPC280065
0.6866 Remote Similarity NPC477049
0.6829 Remote Similarity NPC228638
0.6818 Remote Similarity NPC123669
0.6765 Remote Similarity NPC245650
0.6761 Remote Similarity NPC477106
0.6761 Remote Similarity NPC55068
0.6757 Remote Similarity NPC249713
0.6742 Remote Similarity NPC469739
0.6721 Remote Similarity NPC138935
0.6712 Remote Similarity NPC187315
0.6667 Remote Similarity NPC264417
0.6667 Remote Similarity NPC45313
0.6667 Remote Similarity NPC321030
0.6667 Remote Similarity NPC217095
0.6571 Remote Similarity NPC329003
0.6571 Remote Similarity NPC326524
0.6571 Remote Similarity NPC325550
0.6571 Remote Similarity NPC322186
0.6567 Remote Similarity NPC124382
0.6567 Remote Similarity NPC13011
0.6557 Remote Similarity NPC116934
0.6556 Remote Similarity NPC233273
0.6556 Remote Similarity NPC205546
0.6556 Remote Similarity NPC50902
0.6528 Remote Similarity NPC77891
0.6484 Remote Similarity NPC197294
0.6484 Remote Similarity NPC8098
0.6484 Remote Similarity NPC183449
0.6484 Remote Similarity NPC175614
0.6471 Remote Similarity NPC329686
0.6462 Remote Similarity NPC474460
0.6462 Remote Similarity NPC291437
0.6462 Remote Similarity NPC328784
0.6444 Remote Similarity NPC70323
0.6444 Remote Similarity NPC262312
0.6444 Remote Similarity NPC35269
0.6444 Remote Similarity NPC23454
0.6389 Remote Similarity NPC273614
0.6389 Remote Similarity NPC324077
0.6386 Remote Similarity NPC82799
0.6374 Remote Similarity NPC189764
0.6364 Remote Similarity NPC474495
0.6364 Remote Similarity NPC93639
0.6364 Remote Similarity NPC59408
0.6364 Remote Similarity NPC71053
0.6364 Remote Similarity NPC473672
0.6353 Remote Similarity NPC477199
0.6349 Remote Similarity NPC160628
0.6349 Remote Similarity NPC140501
0.6269 Remote Similarity NPC35756
0.6264 Remote Similarity NPC192066
0.6264 Remote Similarity NPC3568
0.6264 Remote Similarity NPC156782
0.6264 Remote Similarity NPC17290
0.6264 Remote Similarity NPC54961
0.6264 Remote Similarity NPC256570
0.6264 Remote Similarity NPC282088
0.6264 Remote Similarity NPC158445
0.6264 Remote Similarity NPC157353
0.625 Remote Similarity NPC309877
0.625 Remote Similarity NPC476924
0.623 Remote Similarity NPC269823
0.6222 Remote Similarity NPC282705
0.6222 Remote Similarity NPC182632
0.6176 Remote Similarity NPC474496
0.6154 Remote Similarity NPC324638
0.6154 Remote Similarity NPC91044
0.6143 Remote Similarity NPC4881
0.6129 Remote Similarity NPC213538
0.6129 Remote Similarity NPC256766
0.6111 Remote Similarity NPC74672
0.6111 Remote Similarity NPC209047
0.6111 Remote Similarity NPC242503
0.6111 Remote Similarity NPC43074
0.6111 Remote Similarity NPC139782
0.6087 Remote Similarity NPC110732
0.6082 Remote Similarity NPC55336
0.6067 Remote Similarity NPC34754
0.6061 Remote Similarity NPC153538
0.6061 Remote Similarity NPC267110
0.6053 Remote Similarity NPC113224
0.6044 Remote Similarity NPC473604
0.6044 Remote Similarity NPC473950
0.6044 Remote Similarity NPC111567
0.6044 Remote Similarity NPC475125
0.6044 Remote Similarity NPC473581
0.6044 Remote Similarity NPC263545
0.6044 Remote Similarity NPC15851
0.6044 Remote Similarity NPC186840
0.6044 Remote Similarity NPC309898
0.6032 Remote Similarity NPC470439
0.6 Remote Similarity NPC227135
0.598 Remote Similarity NPC29501
0.5977 Remote Similarity NPC475975
0.5972 Remote Similarity NPC210999
0.5972 Remote Similarity NPC181872
0.5972 Remote Similarity NPC226848
0.5972 Remote Similarity NPC325734
0.597 Remote Similarity NPC72699
0.593 Remote Similarity NPC474312
0.5926 Remote Similarity NPC315843
0.5921 Remote Similarity NPC308844
0.5902 Remote Similarity NPC29091
0.5902 Remote Similarity NPC255042
0.5902 Remote Similarity NPC182840
0.5902 Remote Similarity NPC103213
0.59 Remote Similarity NPC315426
0.5897 Remote Similarity NPC23721
0.589 Remote Similarity NPC122239
0.589 Remote Similarity NPC322002
0.5882 Remote Similarity NPC151782
0.5882 Remote Similarity NPC311369
0.5873 Remote Similarity NPC206906
0.5867 Remote Similarity NPC182758
0.5854 Remote Similarity NPC62293
0.5854 Remote Similarity NPC51055
0.5854 Remote Similarity NPC212008
0.5854 Remote Similarity NPC140327
0.5833 Remote Similarity NPC474833
0.5833 Remote Similarity NPC71755
0.5833 Remote Similarity NPC472445
0.5823 Remote Similarity NPC137620
0.5823 Remote Similarity NPC474675
0.5821 Remote Similarity NPC248884
0.5821 Remote Similarity NPC31194
0.5821 Remote Similarity NPC85079
0.5821 Remote Similarity NPC302310
0.5814 Remote Similarity NPC226982
0.5814 Remote Similarity NPC277341
0.5811 Remote Similarity NPC258788
0.5811 Remote Similarity NPC327112
0.58 Remote Similarity NPC201128
0.5795 Remote Similarity NPC161670
0.5781 Remote Similarity NPC86121
0.5775 Remote Similarity NPC281590
0.5765 Remote Similarity NPC471597
0.5765 Remote Similarity NPC157173
0.5765 Remote Similarity NPC314854
0.5765 Remote Similarity NPC313911
0.5758 Remote Similarity NPC35141
0.5758 Remote Similarity NPC124183
0.5758 Remote Similarity NPC157096
0.5758 Remote Similarity NPC180575
0.575 Remote Similarity NPC329904
0.575 Remote Similarity NPC474674
0.575 Remote Similarity NPC473361
0.5747 Remote Similarity NPC224072
0.5747 Remote Similarity NPC39966
0.5735 Remote Similarity NPC474642
0.5735 Remote Similarity NPC249670
0.5735 Remote Similarity NPC473913
0.5735 Remote Similarity NPC199286

  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 NPC129995 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
0.6761 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6349 Remote Similarity NPD4265 Approved
0.6154 Remote Similarity NPD3212 Clinical (unspecified phase)
0.6111 Remote Similarity NPD8522 Clinical (unspecified phase)
0.5862 Remote Similarity NPD205 Approved
0.5846 Remote Similarity NPD860 Phase 2
0.5811 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5761 Remote Similarity NPD6094 Approved
0.5761 Remote Similarity NPD6095 Approved
0.5753 Remote Similarity NPD585 Clinical (unspecified phase)
0.5644 Remote Similarity NPD6640 Phase 3

  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