Structure

Physi-Chem Properties

Molecular Weight:  514.33
Volume:  531.465
LogP:  2.994
LogD:  2.074
LogS:  -2.569
# Rotatable Bonds:  14
TPSA:  151.26
# H-Bond Aceptor:  10
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.204
Synthetic Accessibility Score:  5.232
Fsp3:  0.846
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.284
MDCK Permeability:  6.251047307159752e-05
Pgp-inhibitor:  0.967
Pgp-substrate:  0.95
Human Intestinal Absorption (HIA):  0.66
20% Bioavailability (F20%):  0.993
30% Bioavailability (F30%):  0.825

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.291
Plasma Protein Binding (PPB):  52.04572296142578%
Volume Distribution (VD):  0.775
Pgp-substrate:  39.863948822021484%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.086
CYP2C19-inhibitor:  0.042
CYP2C19-substrate:  0.307
CYP2C9-inhibitor:  0.146
CYP2C9-substrate:  0.05
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.031
CYP3A4-inhibitor:  0.719
CYP3A4-substrate:  0.191

ADMET: Excretion

Clearance (CL):  5.073
Half-life (T1/2):  0.709

ADMET: Toxicity

hERG Blockers:  0.117
Human Hepatotoxicity (H-HT):  0.096
Drug-inuced Liver Injury (DILI):  0.151
AMES Toxicity:  0.809
Rat Oral Acute Toxicity:  0.008
Maximum Recommended Daily Dose:  0.916
Skin Sensitization:  0.973
Carcinogencity:  0.023
Eye Corrosion:  0.003
Eye Irritation:  0.011
Respiratory Toxicity:  0.023

Download Data

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

  Natural Product: NPC28348

Natural Product ID:  NPC28348
Common Name*:   Serratamolide A
IUPAC Name:   (3S,7R,10S,14R)-7,14-diheptyl-3,10-bis(hydroxymethyl)-1,8-dioxa-4,11-diazacyclotetradecane-2,5,9,12-tetrone
Synonyms:  
Standard InCHIKey:  NMEMNUVHBNAERZ-CZYKHXBRSA-N
Standard InCHI:  InChI=1S/C26H46N2O8/c1-3-5-7-9-11-13-19-15-23(31)27-22(18-30)26(34)36-20(14-12-10-8-6-4-2)16-24(32)28-21(17-29)25(33)35-19/h19-22,29-30H,3-18H2,1-2H3,(H,27,31)(H,28,32)/t19-,20-,21+,22+/m1/s1
SMILES:  CCCCCCC[C@@H]1CC(=N[C@@H](CO)C(=O)O[C@H](CCCCCCC)CC(=N[C@@H](CO)C(=O)O1)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL464858
PubChem CID:   168994
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0001813] Peptidomimetics
        • [CHEMONTID:0001961] Depsipeptides
          • [CHEMONTID:0001994] Cyclic depsipeptides

*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
NPO33361 Serratia sp. Species Yersiniaceae Bacteria n.a. n.a. n.a. PMID[18303848]
NPO33361 Serratia sp. Species Yersiniaceae Bacteria n.a. n.a. n.a. PMID[28335605]

☑ 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
NPT4585 Organism Mycobacterium diernhoferi Mycobacterium diernhoferi MIC = 180000.0 nM PMID[509036]
NPT1177 Organism Mycobacterium phlei Mycobacterium phlei MIC = 180000.0 nM PMID[509036]
NPT602 Organism Mycobacterium smegmatis Mycobacterium smegmatis MIC = 180000.0 nM PMID[509036]

☑ 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 NPC28348 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 NPC473985
1.0 High Similarity NPC474298
1.0 High Similarity NPC475808
1.0 High Similarity NPC474299
0.831 Intermediate Similarity NPC43219
0.8289 Intermediate Similarity NPC474312
0.8194 Intermediate Similarity NPC86064
0.7917 Intermediate Similarity NPC477643
0.7917 Intermediate Similarity NPC477641
0.7917 Intermediate Similarity NPC320865
0.7887 Intermediate Similarity NPC477642
0.7887 Intermediate Similarity NPC478256
0.7875 Intermediate Similarity NPC477728
0.7632 Intermediate Similarity NPC316242
0.7595 Intermediate Similarity NPC477730
0.7536 Intermediate Similarity NPC145658
0.7532 Intermediate Similarity NPC473984
0.7532 Intermediate Similarity NPC315535
0.7532 Intermediate Similarity NPC478017
0.7532 Intermediate Similarity NPC315131
0.75 Intermediate Similarity NPC155670
0.75 Intermediate Similarity NPC477644
0.75 Intermediate Similarity NPC95478
0.75 Intermediate Similarity NPC145748
0.7432 Intermediate Similarity NPC474403
0.7407 Intermediate Similarity NPC227051
0.7397 Intermediate Similarity NPC476291
0.7397 Intermediate Similarity NPC476285
0.7302 Intermediate Similarity NPC319110
0.7302 Intermediate Similarity NPC329181
0.7231 Intermediate Similarity NPC270041
0.7206 Intermediate Similarity NPC473599
0.72 Intermediate Similarity NPC141325
0.7176 Intermediate Similarity NPC477729
0.7143 Intermediate Similarity NPC476324
0.7143 Intermediate Similarity NPC476130
0.7105 Intermediate Similarity NPC138435
0.7027 Intermediate Similarity NPC314273
0.7027 Intermediate Similarity NPC474812
0.7027 Intermediate Similarity NPC193280
0.7011 Intermediate Similarity NPC270005
0.7011 Intermediate Similarity NPC208537
0.6951 Remote Similarity NPC47135
0.6901 Remote Similarity NPC145627
0.6892 Remote Similarity NPC470110
0.6883 Remote Similarity NPC476248
0.6825 Remote Similarity NPC319709
0.6825 Remote Similarity NPC289484
0.6795 Remote Similarity NPC472595
0.6757 Remote Similarity NPC470109
0.6667 Remote Similarity NPC474833
0.6625 Remote Similarity NPC472594
0.6622 Remote Similarity NPC326651
0.6622 Remote Similarity NPC325117
0.6622 Remote Similarity NPC322319
0.6622 Remote Similarity NPC474402
0.6622 Remote Similarity NPC470108
0.6579 Remote Similarity NPC472579
0.6567 Remote Similarity NPC329495
0.6506 Remote Similarity NPC314466
0.6447 Remote Similarity NPC195165
0.6404 Remote Similarity NPC39290
0.6404 Remote Similarity NPC159369
0.6383 Remote Similarity NPC220234
0.6292 Remote Similarity NPC292345
0.6292 Remote Similarity NPC193386
0.6269 Remote Similarity NPC90904
0.625 Remote Similarity NPC254541
0.6207 Remote Similarity NPC476523
0.6203 Remote Similarity NPC169976
0.6203 Remote Similarity NPC126366
0.6203 Remote Similarity NPC33267
0.6203 Remote Similarity NPC477200
0.6203 Remote Similarity NPC170963
0.6203 Remote Similarity NPC114640
0.6203 Remote Similarity NPC324165
0.62 Remote Similarity NPC67009
0.6162 Remote Similarity NPC475918
0.6143 Remote Similarity NPC471917
0.6143 Remote Similarity NPC320588
0.6143 Remote Similarity NPC53463
0.6143 Remote Similarity NPC469937
0.6143 Remote Similarity NPC23155
0.6133 Remote Similarity NPC316674
0.6129 Remote Similarity NPC470283
0.6125 Remote Similarity NPC55274
0.6111 Remote Similarity NPC176164
0.6111 Remote Similarity NPC472578
0.6111 Remote Similarity NPC189301
0.6087 Remote Similarity NPC123814
0.6087 Remote Similarity NPC315237
0.6087 Remote Similarity NPC474322
0.6076 Remote Similarity NPC291196
0.6076 Remote Similarity NPC103712
0.6061 Remote Similarity NPC74035
0.6047 Remote Similarity NPC246005
0.6032 Remote Similarity NPC241279
0.6027 Remote Similarity NPC320598
0.6022 Remote Similarity NPC226513
0.602 Remote Similarity NPC301148
0.602 Remote Similarity NPC124554
0.602 Remote Similarity NPC5864
0.6 Remote Similarity NPC327252
0.6 Remote Similarity NPC17455
0.5976 Remote Similarity NPC288086
0.597 Remote Similarity NPC131770
0.597 Remote Similarity NPC200618
0.597 Remote Similarity NPC106872
0.596 Remote Similarity NPC198344
0.5952 Remote Similarity NPC37681
0.5949 Remote Similarity NPC224700
0.5949 Remote Similarity NPC320663
0.5946 Remote Similarity NPC471129
0.5926 Remote Similarity NPC54460
0.5918 Remote Similarity NPC188453
0.5918 Remote Similarity NPC42320
0.5915 Remote Similarity NPC289979
0.5915 Remote Similarity NPC322573
0.5909 Remote Similarity NPC320936
0.5909 Remote Similarity NPC323180
0.5904 Remote Similarity NPC217095
0.5904 Remote Similarity NPC264417
0.59 Remote Similarity NPC124549
0.5897 Remote Similarity NPC118524
0.589 Remote Similarity NPC328447
0.5882 Remote Similarity NPC316807
0.5882 Remote Similarity NPC270805
0.5882 Remote Similarity NPC93888
0.5875 Remote Similarity NPC280065
0.5875 Remote Similarity NPC45060
0.5865 Remote Similarity NPC476875
0.5844 Remote Similarity NPC314103
0.5843 Remote Similarity NPC175419
0.5843 Remote Similarity NPC125253
0.5843 Remote Similarity NPC192025
0.5843 Remote Similarity NPC253975
0.5821 Remote Similarity NPC181588
0.5821 Remote Similarity NPC328497
0.5821 Remote Similarity NPC324004
0.5816 Remote Similarity NPC233932
0.5811 Remote Similarity NPC316826
0.5811 Remote Similarity NPC317143
0.5811 Remote Similarity NPC321536
0.5811 Remote Similarity NPC321468
0.5811 Remote Similarity NPC327748
0.5806 Remote Similarity NPC139782
0.5806 Remote Similarity NPC74672
0.5806 Remote Similarity NPC209047
0.5806 Remote Similarity NPC43074
0.5806 Remote Similarity NPC242503
0.5797 Remote Similarity NPC327239
0.5789 Remote Similarity NPC470665
0.5775 Remote Similarity NPC316889
0.5775 Remote Similarity NPC321118
0.5761 Remote Similarity NPC322966
0.5761 Remote Similarity NPC470284
0.5753 Remote Similarity NPC318260
0.5753 Remote Similarity NPC317147
0.5753 Remote Similarity NPC8979
0.575 Remote Similarity NPC126779
0.5745 Remote Similarity NPC263545
0.5745 Remote Similarity NPC111567
0.5745 Remote Similarity NPC473950
0.5745 Remote Similarity NPC15851
0.5745 Remote Similarity NPC309898
0.5745 Remote Similarity NPC475603
0.5745 Remote Similarity NPC473581
0.5745 Remote Similarity NPC186840
0.5745 Remote Similarity NPC475125
0.5745 Remote Similarity NPC61894
0.5745 Remote Similarity NPC473604
0.5733 Remote Similarity NPC201338
0.5733 Remote Similarity NPC328786
0.5733 Remote Similarity NPC329003
0.5733 Remote Similarity NPC474627
0.5733 Remote Similarity NPC319131
0.5733 Remote Similarity NPC143722
0.5733 Remote Similarity NPC17935
0.5733 Remote Similarity NPC329564
0.5733 Remote Similarity NPC325550
0.5733 Remote Similarity NPC470363
0.5733 Remote Similarity NPC326524
0.5733 Remote Similarity NPC327170
0.5728 Remote Similarity NPC171734
0.5714 Remote Similarity NPC119633
0.5714 Remote Similarity NPC322946
0.5714 Remote Similarity NPC321340
0.5714 Remote Similarity NPC171698
0.5714 Remote Similarity NPC270957
0.5699 Remote Similarity NPC474593
0.5699 Remote Similarity NPC475801
0.5682 Remote Similarity NPC82799
0.5679 Remote Similarity NPC223174
0.5679 Remote Similarity NPC327753
0.5679 Remote Similarity NPC327486
0.5673 Remote Similarity NPC329305
0.5672 Remote Similarity NPC12438
0.5672 Remote Similarity NPC30195
0.5672 Remote Similarity NPC297220
0.567 Remote Similarity NPC134504

  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 NPC28348 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
0.7917 Intermediate Similarity NPD2256 Clinical (unspecified phase)
0.7532 Intermediate Similarity NPD7918 Clinical (unspecified phase)
0.7532 Intermediate Similarity NPD7917 Clinical (unspecified phase)
0.726 Intermediate Similarity NPD3724 Clinical (unspecified phase)
0.7241 Intermediate Similarity NPD8394 Approved
0.6986 Remote Similarity NPD2263 Discontinued
0.6962 Remote Similarity NPD3160 Suspended
0.6951 Remote Similarity NPD7345 Approved
0.6825 Remote Similarity NPD3211 Approved
0.6753 Remote Similarity NPD6944 Clinical (unspecified phase)
0.6667 Remote Similarity NPD1152 Phase 2
0.6625 Remote Similarity NPD2689 Clinical (unspecified phase)
0.65 Remote Similarity NPD1453 Phase 1
0.6471 Remote Similarity NPD9419 Clinical (unspecified phase)
0.6404 Remote Similarity NPD3716 Discontinued
0.6329 Remote Similarity NPD3187 Discontinued
0.6322 Remote Similarity NPD619 Phase 3
0.6316 Remote Similarity NPD5380 Approved
0.6292 Remote Similarity NPD618 Clinical (unspecified phase)
0.6216 Remote Similarity NPD4283 Discontinued
0.617 Remote Similarity NPD6428 Approved
0.6154 Remote Similarity NPD1815 Discontinued
0.6143 Remote Similarity NPD3728 Approved
0.6143 Remote Similarity NPD3730 Approved
0.6139 Remote Similarity NPD6941 Approved
0.6133 Remote Similarity NPD364 Discontinued
0.6098 Remote Similarity NPD376 Approved
0.6098 Remote Similarity NPD11 Approved
0.6087 Remote Similarity NPD3215 Phase 1
0.6081 Remote Similarity NPD574 Approved
0.6076 Remote Similarity NPD8277 Approved
0.6064 Remote Similarity NPD7844 Discontinued
0.6056 Remote Similarity NPD9659 Approved
0.6047 Remote Similarity NPD1448 Clinical (unspecified phase)
0.6 Remote Similarity NPD575 Clinical (unspecified phase)
0.6 Remote Similarity NPD9446 Approved
0.6 Remote Similarity NPD4759 Clinical (unspecified phase)
0.5978 Remote Similarity NPD4780 Clinical (unspecified phase)
0.5949 Remote Similarity NPD8278 Approved
0.5934 Remote Similarity NPD4264 Clinical (unspecified phase)
0.5921 Remote Similarity NPD1151 Approved
0.5915 Remote Similarity NPD4277 Approved
0.5915 Remote Similarity NPD4276 Approved
0.589 Remote Similarity NPD9661 Approved
0.589 Remote Similarity NPD9433 Approved
0.5882 Remote Similarity NPD8624 Approved
0.5859 Remote Similarity NPD7141 Clinical (unspecified phase)
0.5859 Remote Similarity NPD7139 Approved
0.5859 Remote Similarity NPD7140 Approved
0.5851 Remote Similarity NPD1447 Phase 3
0.5851 Remote Similarity NPD1446 Phase 3
0.5844 Remote Similarity NPD1831 Phase 3
0.5833 Remote Similarity NPD4228 Discovery
0.5825 Remote Similarity NPD6413 Approved
0.5825 Remote Similarity NPD8305 Approved
0.5825 Remote Similarity NPD8306 Approved
0.5821 Remote Similarity NPD8810 Clinical (unspecified phase)
0.5806 Remote Similarity NPD8522 Clinical (unspecified phase)
0.58 Remote Similarity NPD8045 Clinical (unspecified phase)
0.5797 Remote Similarity NPD3214 Discontinued
0.5797 Remote Similarity NPD329 Discontinued
0.5795 Remote Similarity NPD883 Phase 2
0.5795 Remote Similarity NPD882 Phase 2
0.575 Remote Similarity NPD4242 Approved
0.5732 Remote Similarity NPD6704 Discontinued
0.5714 Remote Similarity NPD2255 Approved
0.5714 Remote Similarity NPD9441 Phase 2
0.5696 Remote Similarity NPD1429 Clinical (unspecified phase)
0.5684 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5679 Remote Similarity NPD9445 Approved
0.5658 Remote Similarity NPD3193 Approved
0.5658 Remote Similarity NPD3192 Approved
0.5634 Remote Similarity NPD9204 Approved
0.5634 Remote Similarity NPD9205 Approved
0.5634 Remote Similarity NPD9660 Approved
0.5625 Remote Similarity NPD4241 Registered
0.5619 Remote Similarity NPD6421 Discontinued
0.561 Remote Similarity NPD2262 Clinical (unspecified phase)
0.5604 Remote Similarity NPD3723 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