Structure

Physi-Chem Properties

Molecular Weight:  540.34
Volume:  563.421
LogP:  2.598
LogD:  1.9
LogS:  -3.085
# Rotatable Bonds:  15
TPSA:  151.26
# H-Bond Aceptor:  10
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.141
Synthetic Accessibility Score:  5.372
Fsp3:  0.786
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:  -5.305
MDCK Permeability:  7.339990406762809e-05
Pgp-inhibitor:  0.879
Pgp-substrate:  0.705
Human Intestinal Absorption (HIA):  0.645
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.309
Plasma Protein Binding (PPB):  56.30419921875%
Volume Distribution (VD):  0.892
Pgp-substrate:  27.89887809753418%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.083
CYP2C19-inhibitor:  0.045
CYP2C19-substrate:  0.299
CYP2C9-inhibitor:  0.172
CYP2C9-substrate:  0.054
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.035
CYP3A4-inhibitor:  0.832
CYP3A4-substrate:  0.236

ADMET: Excretion

Clearance (CL):  4.755
Half-life (T1/2):  0.81

ADMET: Toxicity

hERG Blockers:  0.172
Human Hepatotoxicity (H-HT):  0.071
Drug-inuced Liver Injury (DILI):  0.045
AMES Toxicity:  0.754
Rat Oral Acute Toxicity:  0.005
Maximum Recommended Daily Dose:  0.927
Skin Sensitization:  0.977
Carcinogencity:  0.028
Eye Corrosion:  0.003
Eye Irritation:  0.011
Respiratory Toxicity:  0.027

Download Data

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

  Natural Product: NPC474312

Natural Product ID:  NPC474312
Common Name*:   Serratamolide B
IUPAC Name:   (3S,7R,10S,14R)-7-heptyl-3,10-bis(hydroxymethyl)-14-[(Z)-non-2-enyl]-1,8-dioxa-4,11-diazacyclotetradecane-2,5,9,12-tetrone
Synonyms:  
Standard InCHIKey:  YMOFMWFDYPVUFF-JYGRAXMSSA-N
Standard InCHI:  InChI=1S/C28H48N2O8/c1-3-5-7-9-10-12-14-16-22-18-26(34)30-23(19-31)27(35)37-21(15-13-11-8-6-4-2)17-25(33)29-24(20-32)28(36)38-22/h12,14,21-24,31-32H,3-11,13,15-20H2,1-2H3,(H,29,33)(H,30,34)/b14-12-/t21-,22-,23+,24+/m1/s1
SMILES:  CCCCCC/C=CC[C@@H]1CC(=N[C@@H](CO)C(=O)O[C@@H](CC(=N[C@H](C(=O)O1)CO)O)CCCCCCC)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL465041
PubChem CID:   44567586
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[555874]
NPT1177 Organism Mycobacterium phlei Mycobacterium phlei MIC = 180000.0 nM PMID[555874]
NPT602 Organism Mycobacterium smegmatis Mycobacterium smegmatis MIC = 180000.0 nM PMID[555874]

☑ 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 NPC474312 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
0.8289 Intermediate Similarity NPC474298
0.8289 Intermediate Similarity NPC475808
0.8289 Intermediate Similarity NPC474299
0.8289 Intermediate Similarity NPC473985
0.8289 Intermediate Similarity NPC28348
0.8049 Intermediate Similarity NPC474833
0.7821 Intermediate Similarity NPC474812
0.7667 Intermediate Similarity NPC39290
0.7667 Intermediate Similarity NPC159369
0.7632 Intermediate Similarity NPC316674
0.75 Intermediate Similarity NPC291196
0.75 Intermediate Similarity NPC103712
0.7374 Intermediate Similarity NPC74035
0.7349 Intermediate Similarity NPC288086
0.73 Intermediate Similarity NPC475918
0.7262 Intermediate Similarity NPC217095
0.7262 Intermediate Similarity NPC264417
0.7237 Intermediate Similarity NPC326524
0.7237 Intermediate Similarity NPC325550
0.7237 Intermediate Similarity NPC329003
0.7143 Intermediate Similarity NPC233932
0.7105 Intermediate Similarity NPC325734
0.7105 Intermediate Similarity NPC321030
0.7073 Intermediate Similarity NPC280065
0.7073 Intermediate Similarity NPC45060
0.7024 Intermediate Similarity NPC43219
0.7021 Intermediate Similarity NPC43074
0.7021 Intermediate Similarity NPC209047
0.7021 Intermediate Similarity NPC74672
0.7021 Intermediate Similarity NPC139782
0.7021 Intermediate Similarity NPC242503
0.6966 Remote Similarity NPC82799
0.6952 Remote Similarity NPC476875
0.6951 Remote Similarity NPC249713
0.6947 Remote Similarity NPC473950
0.6947 Remote Similarity NPC15851
0.6947 Remote Similarity NPC473604
0.6947 Remote Similarity NPC475603
0.6947 Remote Similarity NPC182632
0.6947 Remote Similarity NPC111567
0.6947 Remote Similarity NPC61894
0.6947 Remote Similarity NPC263545
0.6947 Remote Similarity NPC186840
0.6947 Remote Similarity NPC475125
0.6947 Remote Similarity NPC319473
0.6947 Remote Similarity NPC473581
0.6947 Remote Similarity NPC309898
0.6947 Remote Similarity NPC282705
0.6941 Remote Similarity NPC86064
0.6869 Remote Similarity NPC132931
0.6867 Remote Similarity NPC470436
0.6863 Remote Similarity NPC14537
0.6837 Remote Similarity NPC175614
0.6832 Remote Similarity NPC72401
0.6832 Remote Similarity NPC325339
0.6824 Remote Similarity NPC470435
0.6804 Remote Similarity NPC256570
0.6804 Remote Similarity NPC3568
0.6804 Remote Similarity NPC35269
0.6804 Remote Similarity NPC157353
0.6804 Remote Similarity NPC70323
0.6804 Remote Similarity NPC17290
0.6804 Remote Similarity NPC192066
0.6804 Remote Similarity NPC23454
0.6804 Remote Similarity NPC156782
0.6804 Remote Similarity NPC54961
0.6804 Remote Similarity NPC262312
0.6804 Remote Similarity NPC158445
0.6804 Remote Similarity NPC282088
0.6796 Remote Similarity NPC473252
0.6789 Remote Similarity NPC201968
0.6774 Remote Similarity NPC477728
0.6762 Remote Similarity NPC329305
0.6739 Remote Similarity NPC477199
0.6711 Remote Similarity NPC242930
0.6707 Remote Similarity NPC113224
0.6706 Remote Similarity NPC477643
0.6706 Remote Similarity NPC477641
0.6706 Remote Similarity NPC320865
0.67 Remote Similarity NPC234542
0.6699 Remote Similarity NPC205176
0.6667 Remote Similarity NPC45313
0.6667 Remote Similarity NPC197294
0.6667 Remote Similarity NPC478256
0.6667 Remote Similarity NPC183449
0.6667 Remote Similarity NPC8098
0.6667 Remote Similarity NPC477642
0.6637 Remote Similarity NPC45777
0.6637 Remote Similarity NPC477061
0.6635 Remote Similarity NPC201128
0.6634 Remote Similarity NPC473224
0.663 Remote Similarity NPC178758
0.663 Remote Similarity NPC196102
0.6627 Remote Similarity NPC330426
0.6627 Remote Similarity NPC148192
0.6627 Remote Similarity NPC104537
0.6627 Remote Similarity NPC22101
0.6627 Remote Similarity NPC127091
0.6627 Remote Similarity NPC271921
0.6625 Remote Similarity NPC328776
0.6625 Remote Similarity NPC321838
0.6625 Remote Similarity NPC201939
0.6625 Remote Similarity NPC320305
0.6606 Remote Similarity NPC50694
0.6602 Remote Similarity NPC476877
0.6588 Remote Similarity NPC42526
0.6548 Remote Similarity NPC48218
0.6548 Remote Similarity NPC141481
0.6548 Remote Similarity NPC473559
0.6548 Remote Similarity NPC324981
0.6522 Remote Similarity NPC477730
0.6522 Remote Similarity NPC477487
0.6517 Remote Similarity NPC316242
0.6517 Remote Similarity NPC325936
0.6505 Remote Similarity NPC477198
0.65 Remote Similarity NPC243532
0.65 Remote Similarity NPC475503
0.6496 Remote Similarity NPC477793
0.6496 Remote Similarity NPC329919
0.6494 Remote Similarity NPC52264
0.6491 Remote Similarity NPC273185
0.6481 Remote Similarity NPC29501
0.6477 Remote Similarity NPC3094
0.6476 Remote Similarity NPC476876
0.6463 Remote Similarity NPC68343
0.6463 Remote Similarity NPC328089
0.6455 Remote Similarity NPC471645
0.6452 Remote Similarity NPC145748
0.6452 Remote Similarity NPC155670
0.6452 Remote Similarity NPC228638
0.6452 Remote Similarity NPC95478
0.6449 Remote Similarity NPC473578
0.6444 Remote Similarity NPC473984
0.6444 Remote Similarity NPC478017
0.6444 Remote Similarity NPC315535
0.6444 Remote Similarity NPC315131
0.6437 Remote Similarity NPC314678
0.6429 Remote Similarity NPC475443
0.6429 Remote Similarity NPC473829
0.6421 Remote Similarity NPC258824
0.6395 Remote Similarity NPC476660
0.6386 Remote Similarity NPC476657
0.6386 Remote Similarity NPC476655
0.6386 Remote Similarity NPC476654
0.6383 Remote Similarity NPC227051
0.6364 Remote Similarity NPC137538
0.6355 Remote Similarity NPC475150
0.6355 Remote Similarity NPC171734
0.6341 Remote Similarity NPC29697
0.6341 Remote Similarity NPC145658
0.6341 Remote Similarity NPC477106
0.6337 Remote Similarity NPC123141
0.633 Remote Similarity NPC12270
0.6322 Remote Similarity NPC293114
0.6322 Remote Similarity NPC474403
0.631 Remote Similarity NPC476656
0.631 Remote Similarity NPC476659
0.6306 Remote Similarity NPC103391
0.6306 Remote Similarity NPC472536
0.6296 Remote Similarity NPC321919
0.6296 Remote Similarity NPC81896
0.6296 Remote Similarity NPC298484
0.6296 Remote Similarity NPC477644
0.6292 Remote Similarity NPC327041
0.6292 Remote Similarity NPC285840
0.6292 Remote Similarity NPC260396
0.6279 Remote Similarity NPC473772
0.6279 Remote Similarity NPC476285
0.6279 Remote Similarity NPC476291
0.6275 Remote Similarity NPC475646
0.6273 Remote Similarity NPC469865
0.6265 Remote Similarity NPC476658
0.6264 Remote Similarity NPC182292
0.625 Remote Similarity NPC327383
0.625 Remote Similarity NPC185186
0.625 Remote Similarity NPC329914
0.625 Remote Similarity NPC305223
0.625 Remote Similarity NPC329890
0.6235 Remote Similarity NPC26500
0.6235 Remote Similarity NPC99619
0.6228 Remote Similarity NPC169328
0.6224 Remote Similarity NPC477729
0.622 Remote Similarity NPC325929
0.622 Remote Similarity NPC47333
0.622 Remote Similarity NPC271282
0.622 Remote Similarity NPC66460
0.622 Remote Similarity NPC29468
0.6207 Remote Similarity NPC97614
0.6207 Remote Similarity NPC315199
0.6196 Remote Similarity NPC157173
0.619 Remote Similarity NPC477525
0.618 Remote Similarity NPC474321
0.6174 Remote Similarity NPC310467
0.617 Remote Similarity NPC469833
0.617 Remote Similarity NPC469838
0.6168 Remote Similarity NPC271269
0.6168 Remote Similarity NPC258130
0.6163 Remote Similarity NPC209327
0.6163 Remote Similarity NPC273508
0.6162 Remote Similarity NPC319021

  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 NPC474312 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
0.7021 Intermediate Similarity NPD8522 Clinical (unspecified phase)
0.701 Intermediate Similarity NPD4228 Discovery
0.6923 Remote Similarity NPD6413 Approved
0.6875 Remote Similarity NPD5781 Clinical (unspecified phase)
0.6857 Remote Similarity NPD6421 Discontinued
0.6706 Remote Similarity NPD2256 Clinical (unspecified phase)
0.6667 Remote Similarity NPD6095 Approved
0.6667 Remote Similarity NPD6094 Approved
0.6444 Remote Similarity NPD3732 Approved
0.6444 Remote Similarity NPD7917 Clinical (unspecified phase)
0.6444 Remote Similarity NPD7918 Clinical (unspecified phase)
0.633 Remote Similarity NPD1719 Phase 1
0.63 Remote Similarity NPD8394 Approved
0.6222 Remote Similarity NPD818 Approved
0.6222 Remote Similarity NPD819 Approved
0.6163 Remote Similarity NPD3724 Clinical (unspecified phase)
0.6145 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6091 Remote Similarity NPD6420 Discontinued
0.6071 Remote Similarity NPD3197 Phase 1
0.6019 Remote Similarity NPD7839 Suspended
0.6 Remote Similarity NPD7345 Approved
0.5981 Remote Similarity NPD2259 Approved
0.5981 Remote Similarity NPD2258 Approved
0.5978 Remote Similarity NPD3160 Suspended
0.5957 Remote Similarity NPD5790 Clinical (unspecified phase)
0.593 Remote Similarity NPD2263 Discontinued
0.5913 Remote Similarity NPD7505 Discontinued
0.5904 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5895 Remote Similarity NPD5369 Approved
0.5872 Remote Similarity NPD4211 Phase 1
0.5872 Remote Similarity NPD5357 Phase 1
0.5843 Remote Similarity NPD3212 Clinical (unspecified phase)
0.5833 Remote Similarity NPD1407 Approved
0.5784 Remote Similarity NPD7983 Approved
0.5778 Remote Similarity NPD6944 Clinical (unspecified phase)
0.5776 Remote Similarity NPD6936 Clinical (unspecified phase)
0.5776 Remote Similarity NPD6935 Phase 3
0.5773 Remote Similarity NPD7154 Phase 3
0.575 Remote Similarity NPD4266 Approved
0.575 Remote Similarity NPD3194 Approved
0.575 Remote Similarity NPD3195 Phase 2
0.575 Remote Similarity NPD3196 Approved
0.5745 Remote Similarity NPD4271 Approved
0.5745 Remote Similarity NPD4268 Approved
0.5743 Remote Similarity NPD6101 Approved
0.5743 Remote Similarity NPD5764 Clinical (unspecified phase)
0.5714 Remote Similarity NPD4738 Phase 2
0.5702 Remote Similarity NPD8342 Approved
0.5702 Remote Similarity NPD8340 Approved
0.5702 Remote Similarity NPD8341 Approved
0.5702 Remote Similarity NPD8299 Approved
0.5699 Remote Similarity NPD2689 Clinical (unspecified phase)
0.5682 Remote Similarity NPD4247 Clinical (unspecified phase)
0.567 Remote Similarity NPD4270 Approved
0.567 Remote Similarity NPD4269 Approved
0.567 Remote Similarity NPD6435 Approved
0.5663 Remote Similarity NPD6109 Phase 1
0.5658 Remote Similarity NPD3211 Approved
0.5656 Remote Similarity NPD8451 Approved
0.5656 Remote Similarity NPD4816 Clinical (unspecified phase)
0.5647 Remote Similarity NPD6949 Clinical (unspecified phase)
0.5631 Remote Similarity NPD6411 Approved
0.563 Remote Similarity NPD2217 Approved
0.563 Remote Similarity NPD2218 Phase 2
0.5625 Remote Similarity NPD4822 Approved
0.5625 Remote Similarity NPD3172 Approved
0.5625 Remote Similarity NPD4821 Approved
0.5625 Remote Similarity NPD4820 Approved
0.5625 Remote Similarity NPD4252 Approved
0.5625 Remote Similarity NPD4819 Approved
0.5614 Remote Similarity NPD7116 Clinical (unspecified phase)
0.561 Remote Similarity NPD8448 Approved
0.56 Remote Similarity NPD8390 Approved
0.56 Remote Similarity NPD5786 Approved
0.56 Remote Similarity NPD8391 Approved
0.56 Remote Similarity NPD8392 Approved

  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