Structure

Physi-Chem Properties

Molecular Weight:  526.19
Volume:  507.923
LogP:  3.536
LogD:  2.108
LogS:  -4.661
# Rotatable Bonds:  6
TPSA:  102.96
# H-Bond Aceptor:  8
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.399
Synthetic Accessibility Score:  6.147
Fsp3:  0.64
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:  -5.14
MDCK Permeability:  1.77E-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.99
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.009
30% Bioavailability (F30%):  0.981

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.323
Plasma Protein Binding (PPB):  96.08%
Volume Distribution (VD):  1.586
Pgp-substrate:  2.75%

ADMET: Metabolism

CYP1A2-inhibitor:  0.076
CYP1A2-substrate:  0.21
CYP2C19-inhibitor:  0.916
CYP2C19-substrate:  0.465
CYP2C9-inhibitor:  0.917
CYP2C9-substrate:  0.319
CYP2D6-inhibitor:  0.112
CYP2D6-substrate:  0.848
CYP3A4-inhibitor:  0.949
CYP3A4-substrate:  0.369

ADMET: Excretion

Clearance (CL):  5.893
Half-life (T1/2):  0.346

ADMET: Toxicity

hERG Blockers:  0.568
Human Hepatotoxicity (H-HT):  0.976
Drug-inuced Liver Injury (DILI):  0.933
AMES Toxicity:  0.968
Rat Oral Acute Toxicity:  0.765
Maximum Recommended Daily Dose:  0.994
Skin Sensitization:  0.958
Carcinogencity:  0.055
Eye Corrosion:  0.003
Eye Irritation:  0.009
Respiratory Toxicity:  0.954

Download Data

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

  Natural Product: NPC477553

Natural Product ID:  NPC477553
Common Name*:   [(1R,4Z,8E,10Z,12S,15R,17S)-5,12-dimethyl-3-oxo-17-[(4R)-2-oxo-1,3-thiazolidin-4-yl]-2,16-dioxabicyclo[13.3.1]nonadeca-4,8,10-trien-17-yl] N-(2-chloroethyl)carbamate
IUPAC Name:   [(1R,4Z,8E,10Z,12S,15R,17S)-5,12-dimethyl-3-oxo-17-[(4R)-2-oxo-1,3-thiazolidin-4-yl]-2,16-dioxabicyclo[13.3.1]nonadeca-4,8,10-trien-17-yl] N-(2-chloroethyl)carbamate
Synonyms:  
Standard InCHIKey:  CHHHDCFJTWVFPK-ODVPECJOSA-N
Standard InCHI:  InChI=1S/C25H35ClN2O6S/c1-17-7-5-3-4-6-8-18(2)13-22(29)32-20-14-19(10-9-17)33-25(15-20,21-16-35-24(31)28-21)34-23(30)27-12-11-26/h3-5,7,13,17,19-21H,6,8-12,14-16H2,1-2H3,(H,27,30)(H,28,31)/b4-3+,7-5-,18-13-/t17-,19-,20-,21+,25+/m1/s1
SMILES:  C[C@H]/1CC[C@@H]2C[C@H](C[C@@](O2)([C@@H]3CSC(=O)N3)OC(=O)NCCCl)OC(=O)/C=C(\CC/C=C/C=C1)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   24853747
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000147] Macrolides and analogues

*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
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota n.a. n.a. n.a. PMID[15217296]
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota n.a. n.a. n.a. PMID[16499319]
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota n.a. sand-covered bottom at -10 to -15 m at Hurghada, on the Egyptian Red Sea coast 2003-JUN PMID[18298079]
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota n.a. n.a. n.a. PMID[18942825]
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ 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
NPT396 Cell Line T47D Homo sapiens Activity < 20 % PMID[18298079]
NPT83 Cell Line MCF7 Homo sapiens IC50 = 57809604.74 nM PMID[20684858]
NPT2 Others Unspecified Inhibition < 50 % PMID[18298079]

☑ 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 NPC477553 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
0.9907 High Similarity NPC477555
0.9252 High Similarity NPC476034
0.9252 High Similarity NPC474969
0.9189 High Similarity NPC477554
0.9159 High Similarity NPC250187
0.9074 High Similarity NPC471636
0.9074 High Similarity NPC287572
0.8889 High Similarity NPC101106
0.8889 High Similarity NPC135216
0.8818 High Similarity NPC474891
0.8673 High Similarity NPC475988
0.8584 High Similarity NPC295444
0.8584 High Similarity NPC268327
0.8584 High Similarity NPC273215
0.8584 High Similarity NPC279383
0.8571 High Similarity NPC127578
0.8349 Intermediate Similarity NPC474873
0.7669 Intermediate Similarity NPC477557
0.7647 Intermediate Similarity NPC474995
0.7521 Intermediate Similarity NPC474984
0.7286 Intermediate Similarity NPC477556
0.672 Remote Similarity NPC29501
0.6719 Remote Similarity NPC201968
0.6562 Remote Similarity NPC50694
0.6471 Remote Similarity NPC475503
0.6454 Remote Similarity NPC230889
0.6429 Remote Similarity NPC329305
0.6417 Remote Similarity NPC475646
0.6393 Remote Similarity NPC175531
0.6357 Remote Similarity NPC78189
0.6348 Remote Similarity NPC316138
0.6348 Remote Similarity NPC313658
0.6336 Remote Similarity NPC65045
0.632 Remote Similarity NPC472433
0.632 Remote Similarity NPC475918
0.629 Remote Similarity NPC55336
0.6279 Remote Similarity NPC469865
0.6279 Remote Similarity NPC43648
0.6259 Remote Similarity NPC477988
0.625 Remote Similarity NPC122926
0.625 Remote Similarity NPC113012
0.624 Remote Similarity NPC75523
0.6204 Remote Similarity NPC329401
0.6204 Remote Similarity NPC477987
0.6198 Remote Similarity NPC175614
0.6172 Remote Similarity NPC473578
0.6148 Remote Similarity NPC470000
0.6142 Remote Similarity NPC315426
0.6115 Remote Similarity NPC477793
0.6115 Remote Similarity NPC329919
0.6098 Remote Similarity NPC270813
0.6094 Remote Similarity NPC475150
0.609 Remote Similarity NPC469997
0.6068 Remote Similarity NPC199382
0.6066 Remote Similarity NPC183449
0.6066 Remote Similarity NPC197294
0.6066 Remote Similarity NPC8098
0.6061 Remote Similarity NPC471645
0.6058 Remote Similarity NPC323168
0.6058 Remote Similarity NPC477990
0.6058 Remote Similarity NPC477989
0.6058 Remote Similarity NPC111162
0.6058 Remote Similarity NPC293550
0.6047 Remote Similarity NPC24389
0.6034 Remote Similarity NPC471494
0.6029 Remote Similarity NPC469515
0.6016 Remote Similarity NPC4834
0.6 Remote Similarity NPC477986
0.6 Remote Similarity NPC138534
0.5984 Remote Similarity NPC477000
0.5984 Remote Similarity NPC477001
0.5984 Remote Similarity NPC205176
0.5968 Remote Similarity NPC203627
0.5965 Remote Similarity NPC184208
0.5965 Remote Similarity NPC471552
0.5965 Remote Similarity NPC473339
0.5965 Remote Similarity NPC8538
0.5954 Remote Similarity NPC12270
0.5952 Remote Similarity NPC473289
0.5952 Remote Similarity NPC477198
0.5942 Remote Similarity NPC16709
0.5942 Remote Similarity NPC315783
0.5935 Remote Similarity NPC45313
0.5935 Remote Similarity NPC288350
0.5935 Remote Similarity NPC173329
0.5929 Remote Similarity NPC139712
0.5923 Remote Similarity NPC133625
0.592 Remote Similarity NPC474985
0.5917 Remote Similarity NPC477866
0.5917 Remote Similarity NPC477865
0.5902 Remote Similarity NPC17290
0.5902 Remote Similarity NPC158445
0.5902 Remote Similarity NPC192066
0.5902 Remote Similarity NPC282088
0.5902 Remote Similarity NPC54961
0.5902 Remote Similarity NPC156782
0.5902 Remote Similarity NPC256368
0.5902 Remote Similarity NPC157353
0.5902 Remote Similarity NPC256570
0.5902 Remote Similarity NPC3568
0.5899 Remote Similarity NPC471087
0.5899 Remote Similarity NPC469494
0.5899 Remote Similarity NPC326386
0.5899 Remote Similarity NPC204639
0.5899 Remote Similarity NPC477985
0.5882 Remote Similarity NPC67917
0.5882 Remote Similarity NPC313802
0.5882 Remote Similarity NPC314268
0.5882 Remote Similarity NPC477515
0.5868 Remote Similarity NPC319473
0.5868 Remote Similarity NPC206679
0.5868 Remote Similarity NPC476084
0.5868 Remote Similarity NPC114172
0.5868 Remote Similarity NPC476075
0.5868 Remote Similarity NPC471324
0.5862 Remote Similarity NPC31019
0.5862 Remote Similarity NPC27314
0.5862 Remote Similarity NPC2379
0.5862 Remote Similarity NPC263087
0.5862 Remote Similarity NPC106912
0.5859 Remote Similarity NPC74035
0.5852 Remote Similarity NPC316325
0.5847 Remote Similarity NPC311163
0.5841 Remote Similarity NPC474833
0.5827 Remote Similarity NPC72401
0.5827 Remote Similarity NPC325339
0.5826 Remote Similarity NPC315731
0.582 Remote Similarity NPC472196
0.582 Remote Similarity NPC109406
0.582 Remote Similarity NPC159092
0.582 Remote Similarity NPC238090
0.582 Remote Similarity NPC472195
0.5816 Remote Similarity NPC314282
0.5814 Remote Similarity NPC82251
0.5812 Remote Similarity NPC266718
0.5809 Remote Similarity NPC9714
0.5804 Remote Similarity NPC469880
0.5796 Remote Similarity NPC473208
0.5794 Remote Similarity NPC477721
0.5794 Remote Similarity NPC477716
0.5789 Remote Similarity NPC261750
0.5789 Remote Similarity NPC477088
0.5789 Remote Similarity NPC1111
0.5786 Remote Similarity NPC469999
0.5785 Remote Similarity NPC74672
0.5785 Remote Similarity NPC202886
0.5785 Remote Similarity NPC139782
0.5785 Remote Similarity NPC209047
0.5785 Remote Similarity NPC43074
0.5785 Remote Similarity NPC242503
0.5785 Remote Similarity NPC471569
0.5781 Remote Similarity NPC45897
0.5778 Remote Similarity NPC30196
0.5776 Remote Similarity NPC163365
0.5775 Remote Similarity NPC173173
0.5775 Remote Similarity NPC471086
0.5772 Remote Similarity NPC35269
0.5772 Remote Similarity NPC477722
0.5772 Remote Similarity NPC70323
0.5772 Remote Similarity NPC262312
0.5772 Remote Similarity NPC159698
0.5772 Remote Similarity NPC23454
0.5762 Remote Similarity NPC160222
0.5762 Remote Similarity NPC193753
0.576 Remote Similarity NPC476344
0.576 Remote Similarity NPC52820
0.5758 Remote Similarity NPC477997
0.5752 Remote Similarity NPC477203
0.5748 Remote Similarity NPC471637
0.5748 Remote Similarity NPC475157
0.5748 Remote Similarity NPC313234
0.5748 Remote Similarity NPC154132
0.5748 Remote Similarity NPC475655
0.5748 Remote Similarity NPC477717
0.5748 Remote Similarity NPC198992
0.5748 Remote Similarity NPC2313
0.5748 Remote Similarity NPC57586
0.5739 Remote Similarity NPC311369
0.5738 Remote Similarity NPC469410
0.5738 Remote Similarity NPC263545
0.5738 Remote Similarity NPC15851
0.5738 Remote Similarity NPC186840
0.5738 Remote Similarity NPC61894
0.5738 Remote Similarity NPC473581
0.5738 Remote Similarity NPC111567
0.5738 Remote Similarity NPC473950
0.5738 Remote Similarity NPC475125
0.5738 Remote Similarity NPC475603
0.5738 Remote Similarity NPC309898
0.5738 Remote Similarity NPC473604
0.5736 Remote Similarity NPC14537
0.5735 Remote Similarity NPC6531
0.5726 Remote Similarity NPC189764
0.5726 Remote Similarity NPC205546
0.5726 Remote Similarity NPC233273
0.5726 Remote Similarity NPC150041
0.5726 Remote Similarity NPC50902
0.5726 Remote Similarity NPC300710
0.5724 Remote Similarity NPC314361
0.5714 Remote Similarity NPC132931

  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 NPC477553 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
0.8889 High Similarity NPD4211 Phase 1
0.6589 Remote Similarity NPD7505 Discontinued
0.6198 Remote Similarity NPD4228 Discovery
0.6067 Remote Similarity NPD7625 Phase 1
0.6047 Remote Similarity NPD6413 Approved
0.5954 Remote Similarity NPD1719 Phase 1
0.5942 Remote Similarity NPD7829 Approved
0.5942 Remote Similarity NPD7830 Approved
0.5926 Remote Similarity NPD7641 Discontinued
0.5915 Remote Similarity NPD6914 Discontinued
0.5915 Remote Similarity NPD8391 Approved
0.5915 Remote Similarity NPD8390 Approved
0.5915 Remote Similarity NPD8392 Approved
0.5878 Remote Similarity NPD6421 Discontinued
0.5857 Remote Similarity NPD8451 Approved
0.5852 Remote Similarity NPD7500 Approved
0.584 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5816 Remote Similarity NPD8448 Approved
0.5797 Remote Similarity NPD8444 Approved
0.5785 Remote Similarity NPD8522 Clinical (unspecified phase)
0.5785 Remote Similarity NPD6095 Approved
0.5785 Remote Similarity NPD6094 Approved
0.5714 Remote Similarity NPD7642 Approved
0.568 Remote Similarity NPD7839 Suspended
0.5674 Remote Similarity NPD8341 Approved
0.5674 Remote Similarity NPD8342 Approved
0.5674 Remote Similarity NPD8340 Approved
0.5674 Remote Similarity NPD8299 Approved
0.5659 Remote Similarity NPD2258 Approved
0.5659 Remote Similarity NPD2259 Approved
0.5656 Remote Similarity NPD7838 Discovery
0.5634 Remote Similarity NPD8273 Phase 1

  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