Structure

Physi-Chem Properties

Molecular Weight:  570.14
Volume:  511.995
LogP:  3.8
LogD:  3.039
LogS:  -4.799
# 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:  0.362
Synthetic Accessibility Score:  6.184
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:  -4.969
MDCK Permeability:  1.16E-05
Pgp-inhibitor:  0.581
Pgp-substrate:  0.949
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.968

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.316
Plasma Protein Binding (PPB):  95.20%
Volume Distribution (VD):  1.423
Pgp-substrate:  3.22%

ADMET: Metabolism

CYP1A2-inhibitor:  0.061
CYP1A2-substrate:  0.221
CYP2C19-inhibitor:  0.89
CYP2C19-substrate:  0.42
CYP2C9-inhibitor:  0.903
CYP2C9-substrate:  0.322
CYP2D6-inhibitor:  0.104
CYP2D6-substrate:  0.862
CYP3A4-inhibitor:  0.946
CYP3A4-substrate:  0.328

ADMET: Excretion

Clearance (CL):  3.871
Half-life (T1/2):  0.2

ADMET: Toxicity

hERG Blockers:  0.404
Human Hepatotoxicity (H-HT):  0.964
Drug-inuced Liver Injury (DILI):  0.945
AMES Toxicity:  0.971
Rat Oral Acute Toxicity:  0.686
Maximum Recommended Daily Dose:  0.995
Skin Sensitization:  0.965
Carcinogencity:  0.061
Eye Corrosion:  0.003
Eye Irritation:  0.01
Respiratory Toxicity:  0.941

Download Data

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

  Natural Product: NPC477554

Natural Product ID:  NPC477554
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-bromoethyl)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-bromoethyl)carbamate
Synonyms:  
Standard InCHIKey:  ZPHSMQHQJGJQEQ-ODVPECJOSA-N
Standard InCHI:  InChI=1S/C25H35BrN2O6S/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)NCCBr)OC(=O)/C=C(\CC/C=C/C=C1)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   24853809
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 = 51522864.46 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 NPC477554 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
0.934 High Similarity NPC474969
0.934 High Similarity NPC476034
0.9245 High Similarity NPC250187
0.9189 High Similarity NPC477553
0.9159 High Similarity NPC471636
0.9159 High Similarity NPC287572
0.9107 High Similarity NPC477555
0.8972 High Similarity NPC135216
0.8972 High Similarity NPC101106
0.8899 High Similarity NPC474891
0.875 High Similarity NPC475988
0.8661 High Similarity NPC279383
0.8661 High Similarity NPC295444
0.8661 High Similarity NPC273215
0.8661 High Similarity NPC268327
0.8649 High Similarity NPC127578
0.8426 Intermediate Similarity NPC474873
0.7727 Intermediate Similarity NPC477557
0.7712 Intermediate Similarity NPC474995
0.7583 Intermediate Similarity NPC474984
0.7338 Intermediate Similarity NPC477556
0.6774 Remote Similarity NPC29501
0.6772 Remote Similarity NPC201968
0.6614 Remote Similarity NPC50694
0.6525 Remote Similarity NPC475503
0.648 Remote Similarity NPC329305
0.6471 Remote Similarity NPC475646
0.6446 Remote Similarity NPC175531
0.6404 Remote Similarity NPC316138
0.6404 Remote Similarity NPC313658
0.6385 Remote Similarity NPC65045
0.6371 Remote Similarity NPC475918
0.6341 Remote Similarity NPC55336
0.6328 Remote Similarity NPC43648
0.6328 Remote Similarity NPC469865
0.6304 Remote Similarity NPC477988
0.6299 Remote Similarity NPC122926
0.6299 Remote Similarity NPC113012
0.629 Remote Similarity NPC75523
0.625 Remote Similarity NPC329401
0.625 Remote Similarity NPC477987
0.625 Remote Similarity NPC175614
0.622 Remote Similarity NPC473578
0.6194 Remote Similarity NPC470000
0.619 Remote Similarity NPC315426
0.6159 Remote Similarity NPC477793
0.6159 Remote Similarity NPC329919
0.6148 Remote Similarity NPC270813
0.6142 Remote Similarity NPC475150
0.6136 Remote Similarity NPC469997
0.6121 Remote Similarity NPC199382
0.6116 Remote Similarity NPC197294
0.6116 Remote Similarity NPC183449
0.6116 Remote Similarity NPC8098
0.6107 Remote Similarity NPC471645
0.6103 Remote Similarity NPC477990
0.6103 Remote Similarity NPC477989
0.6103 Remote Similarity NPC323168
0.6103 Remote Similarity NPC293550
0.6103 Remote Similarity NPC111162
0.6094 Remote Similarity NPC24389
0.6087 Remote Similarity NPC471494
0.6074 Remote Similarity NPC469515
0.6066 Remote Similarity NPC4834
0.6045 Remote Similarity NPC477986
0.6045 Remote Similarity NPC138534
0.6032 Remote Similarity NPC477001
0.6032 Remote Similarity NPC205176
0.6032 Remote Similarity NPC477000
0.6018 Remote Similarity NPC471552
0.6018 Remote Similarity NPC473339
0.6018 Remote Similarity NPC184208
0.6018 Remote Similarity NPC8538
0.6016 Remote Similarity NPC203627
0.6 Remote Similarity NPC477198
0.6 Remote Similarity NPC473289
0.5985 Remote Similarity NPC315783
0.5984 Remote Similarity NPC173329
0.5984 Remote Similarity NPC472433
0.5984 Remote Similarity NPC288350
0.5984 Remote Similarity NPC45313
0.5982 Remote Similarity NPC139712
0.5969 Remote Similarity NPC133625
0.5968 Remote Similarity NPC474985
0.5966 Remote Similarity NPC477865
0.5966 Remote Similarity NPC477866
0.595 Remote Similarity NPC282088
0.595 Remote Similarity NPC158445
0.595 Remote Similarity NPC157353
0.595 Remote Similarity NPC3568
0.595 Remote Similarity NPC256368
0.595 Remote Similarity NPC192066
0.595 Remote Similarity NPC156782
0.595 Remote Similarity NPC17290
0.595 Remote Similarity NPC256570
0.595 Remote Similarity NPC54961
0.5942 Remote Similarity NPC326386
0.5942 Remote Similarity NPC469494
0.5942 Remote Similarity NPC471087
0.5942 Remote Similarity NPC477985
0.5931 Remote Similarity NPC230889
0.5926 Remote Similarity NPC314268
0.5926 Remote Similarity NPC67917
0.5926 Remote Similarity NPC477515
0.5926 Remote Similarity NPC313802
0.5917 Remote Similarity NPC471324
0.5917 Remote Similarity NPC206679
0.5917 Remote Similarity NPC476075
0.5917 Remote Similarity NPC114172
0.5917 Remote Similarity NPC476084
0.5917 Remote Similarity NPC319473
0.5913 Remote Similarity NPC27314
0.5913 Remote Similarity NPC31019
0.5913 Remote Similarity NPC2379
0.5913 Remote Similarity NPC263087
0.5913 Remote Similarity NPC106912
0.5906 Remote Similarity NPC469869
0.5906 Remote Similarity NPC74035
0.5897 Remote Similarity NPC311163
0.5896 Remote Similarity NPC316325
0.5893 Remote Similarity NPC474833
0.5877 Remote Similarity NPC315731
0.5873 Remote Similarity NPC325339
0.5873 Remote Similarity NPC72401
0.5868 Remote Similarity NPC238090
0.5868 Remote Similarity NPC159092
0.5868 Remote Similarity NPC472196
0.5868 Remote Similarity NPC472195
0.5868 Remote Similarity NPC109406
0.5862 Remote Similarity NPC266718
0.5859 Remote Similarity NPC82251
0.5857 Remote Similarity NPC314282
0.5856 Remote Similarity NPC469880
0.5852 Remote Similarity NPC9714
0.584 Remote Similarity NPC477716
0.584 Remote Similarity NPC477721
0.5833 Remote Similarity NPC78189
0.5833 Remote Similarity NPC1111
0.5833 Remote Similarity NPC261750
0.5833 Remote Similarity NPC202886
0.5833 Remote Similarity NPC242503
0.5833 Remote Similarity NPC139782
0.5833 Remote Similarity NPC471569
0.5833 Remote Similarity NPC74672
0.5833 Remote Similarity NPC209047
0.5833 Remote Similarity NPC43074
0.5833 Remote Similarity NPC473208
0.5827 Remote Similarity NPC45897
0.5827 Remote Similarity NPC469999
0.5821 Remote Similarity NPC30196
0.582 Remote Similarity NPC477722
0.582 Remote Similarity NPC23454
0.582 Remote Similarity NPC262312
0.582 Remote Similarity NPC35269
0.582 Remote Similarity NPC70323
0.582 Remote Similarity NPC159698
0.5816 Remote Similarity NPC173173
0.5816 Remote Similarity NPC471086
0.5813 Remote Similarity NPC163365
0.5806 Remote Similarity NPC52820
0.5806 Remote Similarity NPC476344
0.5804 Remote Similarity NPC477203
0.5802 Remote Similarity NPC477997
0.58 Remote Similarity NPC193753
0.58 Remote Similarity NPC160222
0.5794 Remote Similarity NPC2313
0.5794 Remote Similarity NPC477717
0.5794 Remote Similarity NPC198992
0.5794 Remote Similarity NPC57586
0.5794 Remote Similarity NPC313234
0.5794 Remote Similarity NPC471637
0.5794 Remote Similarity NPC475157
0.5794 Remote Similarity NPC475655
0.5794 Remote Similarity NPC154132
0.5789 Remote Similarity NPC311369
0.5785 Remote Similarity NPC263545
0.5785 Remote Similarity NPC475603
0.5785 Remote Similarity NPC473950
0.5785 Remote Similarity NPC475125
0.5785 Remote Similarity NPC473604
0.5785 Remote Similarity NPC473581
0.5785 Remote Similarity NPC61894
0.5785 Remote Similarity NPC15851
0.5785 Remote Similarity NPC186840
0.5785 Remote Similarity NPC309898
0.5785 Remote Similarity NPC111567
0.5785 Remote Similarity NPC469410
0.5781 Remote Similarity NPC14537
0.5778 Remote Similarity NPC6531
0.5772 Remote Similarity NPC150041
0.5772 Remote Similarity NPC50902
0.5772 Remote Similarity NPC300710
0.5772 Remote Similarity NPC233273
0.5772 Remote Similarity NPC205546
0.5772 Remote Similarity NPC189764
0.5764 Remote Similarity NPC314361
0.5763 Remote Similarity NPC61527
0.5763 Remote Similarity NPC208473
0.576 Remote Similarity NPC132931
0.5758 Remote Similarity NPC21713

  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 NPC477554 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
0.8972 High Similarity NPD4211 Phase 1
0.6641 Remote Similarity NPD7505 Discontinued
0.625 Remote Similarity NPD4228 Discovery
0.6107 Remote Similarity NPD7625 Phase 1
0.6094 Remote Similarity NPD6413 Approved
0.5985 Remote Similarity NPD7829 Approved
0.5985 Remote Similarity NPD7830 Approved
0.597 Remote Similarity NPD7641 Discontinued
0.5957 Remote Similarity NPD6914 Discontinued
0.5957 Remote Similarity NPD8392 Approved
0.5957 Remote Similarity NPD8391 Approved
0.5957 Remote Similarity NPD8390 Approved
0.5923 Remote Similarity NPD6421 Discontinued
0.5899 Remote Similarity NPD8451 Approved
0.5896 Remote Similarity NPD7500 Approved
0.5887 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5857 Remote Similarity NPD8448 Approved
0.5839 Remote Similarity NPD8444 Approved
0.5833 Remote Similarity NPD8522 Clinical (unspecified phase)
0.5833 Remote Similarity NPD6094 Approved
0.5833 Remote Similarity NPD6095 Approved
0.5755 Remote Similarity NPD7642 Approved
0.5726 Remote Similarity NPD7839 Suspended
0.5714 Remote Similarity NPD8341 Approved
0.5714 Remote Similarity NPD8340 Approved
0.5714 Remote Similarity NPD8299 Approved
0.5714 Remote Similarity NPD8342 Approved
0.5703 Remote Similarity NPD2258 Approved
0.5703 Remote Similarity NPD2259 Approved
0.5702 Remote Similarity NPD7838 Discovery
0.5674 Remote Similarity NPD8273 Phase 1
0.5639 Remote Similarity NPD7116 Clinical (unspecified phase)
0.561 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5603 Remote Similarity NPD4480 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