Structure

Physi-Chem Properties

Molecular Weight:  453.84
Volume:  289.967
LogP:  4.408
LogD:  2.443
LogS:  -3.691
# Rotatable Bonds:  2
TPSA:  57.53
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.501
Synthetic Accessibility Score:  3.467
Fsp3:  0.462
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.753
MDCK Permeability:  1.8921833543572575e-05
Pgp-inhibitor:  0.603
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.495
20% Bioavailability (F20%):  0.027
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.26
Plasma Protein Binding (PPB):  100.28917694091797%
Volume Distribution (VD):  2.181
Pgp-substrate:  1.1642838716506958%

ADMET: Metabolism

CYP1A2-inhibitor:  0.855
CYP1A2-substrate:  0.513
CYP2C19-inhibitor:  0.237
CYP2C19-substrate:  0.07
CYP2C9-inhibitor:  0.786
CYP2C9-substrate:  0.885
CYP2D6-inhibitor:  0.037
CYP2D6-substrate:  0.466
CYP3A4-inhibitor:  0.133
CYP3A4-substrate:  0.166

ADMET: Excretion

Clearance (CL):  1.365
Half-life (T1/2):  0.783

ADMET: Toxicity

hERG Blockers:  0.008
Human Hepatotoxicity (H-HT):  0.225
Drug-inuced Liver Injury (DILI):  0.422
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.429
Maximum Recommended Daily Dose:  0.11
Skin Sensitization:  0.806
Carcinogencity:  0.103
Eye Corrosion:  0.013
Eye Irritation:  0.663
Respiratory Toxicity:  0.607

Download Data

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

  Natural Product: NPC105702

Natural Product ID:  NPC105702
Common Name*:   Symphyoketone
IUPAC Name:   (2R)-2-[(2,3,6-tribromo-4,5-dihydroxyphenyl)methyl]cyclohexan-1-one
Synonyms:   symphyoketone
Standard InCHIKey:  LLMBLIAKCCQZSI-ZCFIWIBFSA-N
Standard InCHI:  InChI=1S/C13H13Br3O3/c14-9-7(5-6-3-1-2-4-8(6)17)10(15)12(18)13(19)11(9)16/h6,18-19H,1-5H2/t6-/m1/s1
SMILES:  C1CCC(=O)[C@H](C1)Cc1c(c(c(c(c1Br)O)O)Br)Br
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL490356
PubChem CID:   10366827
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000134] Phenols
        • [CHEMONTID:0001286] Benzenediols
          • [CHEMONTID:0000135] Catechols

*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
NPO6092 Symphyocladia latiuscula Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[11141124]
NPO6092 Symphyocladia latiuscula Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[15844965]
NPO6092 Symphyocladia latiuscula Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[17602526]
NPO6092 Symphyocladia latiuscula Species Rhodomelaceae 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
NPT233 Individual Protein Carbonic anhydrase II Homo sapiens Ki = 560.0 nM PMID[512629]
NPT1062 Individual Protein Carbonic anhydrase IV Homo sapiens Ki = 1080.0 nM PMID[512629]
NPT1063 Individual Protein Carbonic anhydrase VI Homo sapiens Ki = 590.0 nM PMID[512629]
NPT1 Others Radical scavenging activity IC50 = 8500.0 nM PMID[512628]
NPT947 Individual Protein Carbonic anhydrase I Homo sapiens Ki = 1670.0 nM PMID[512629]

☑ 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 NPC105702 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
0.904 High Similarity NPC84606
0.896 High Similarity NPC219444
0.8618 High Similarity NPC50782
0.8615 High Similarity NPC13004
0.837 Intermediate Similarity NPC471328
0.8359 Intermediate Similarity NPC227976
0.8358 Intermediate Similarity NPC110800
0.8321 Intermediate Similarity NPC220311
0.8162 Intermediate Similarity NPC303011
0.8129 Intermediate Similarity NPC168680
0.812 Intermediate Similarity NPC134219
0.8045 Intermediate Similarity NPC142776
0.797 Intermediate Similarity NPC137117
0.7923 Intermediate Similarity NPC38483
0.7872 Intermediate Similarity NPC271942
0.7868 Intermediate Similarity NPC55113
0.7842 Intermediate Similarity NPC244890
0.7842 Intermediate Similarity NPC163560
0.7737 Intermediate Similarity NPC150929
0.773 Intermediate Similarity NPC199089
0.7697 Intermediate Similarity NPC474535
0.7687 Intermediate Similarity NPC47790
0.7676 Intermediate Similarity NPC224663
0.7647 Intermediate Similarity NPC475697
0.7643 Intermediate Similarity NPC474135
0.7594 Intermediate Similarity NPC474146
0.7569 Intermediate Similarity NPC160932
0.7554 Intermediate Similarity NPC85049
0.7554 Intermediate Similarity NPC474614
0.7535 Intermediate Similarity NPC245386
0.7519 Intermediate Similarity NPC117759
0.75 Intermediate Similarity NPC226493
0.75 Intermediate Similarity NPC135103
0.75 Intermediate Similarity NPC160081
0.7467 Intermediate Similarity NPC226514
0.7466 Intermediate Similarity NPC118794
0.7466 Intermediate Similarity NPC89341
0.7464 Intermediate Similarity NPC43706
0.7429 Intermediate Similarity NPC474536
0.741 Intermediate Similarity NPC473708
0.741 Intermediate Similarity NPC474147
0.7315 Intermediate Similarity NPC109346
0.7292 Intermediate Similarity NPC312155
0.7287 Intermediate Similarity NPC54543
0.7237 Intermediate Similarity NPC473608
0.7234 Intermediate Similarity NPC214553
0.7231 Intermediate Similarity NPC473358
0.7226 Intermediate Similarity NPC136543
0.7206 Intermediate Similarity NPC180207
0.7164 Intermediate Similarity NPC79844
0.7153 Intermediate Similarity NPC300678
0.7152 Intermediate Similarity NPC84426
0.7143 Intermediate Similarity NPC156356
0.7083 Intermediate Similarity NPC43613
0.7077 Intermediate Similarity NPC471495
0.7073 Intermediate Similarity NPC475466
0.7068 Intermediate Similarity NPC471488
0.7067 Intermediate Similarity NPC184632
0.705 Intermediate Similarity NPC229213
0.7 Intermediate Similarity NPC474169
0.7 Intermediate Similarity NPC473572
0.694 Remote Similarity NPC33244
0.6912 Remote Similarity NPC61062
0.6912 Remote Similarity NPC277394
0.6912 Remote Similarity NPC299252
0.6906 Remote Similarity NPC471486
0.6889 Remote Similarity NPC94217
0.6859 Remote Similarity NPC152947
0.6849 Remote Similarity NPC259017
0.6842 Remote Similarity NPC222084
0.6835 Remote Similarity NPC265454
0.6835 Remote Similarity NPC34634
0.6809 Remote Similarity NPC116562
0.6786 Remote Similarity NPC98305
0.6776 Remote Similarity NPC250597
0.6774 Remote Similarity NPC88896
0.6763 Remote Similarity NPC100395
0.6733 Remote Similarity NPC177967
0.6733 Remote Similarity NPC471237
0.6718 Remote Similarity NPC239291
0.6716 Remote Similarity NPC471487
0.6713 Remote Similarity NPC15127
0.6691 Remote Similarity NPC148969
0.669 Remote Similarity NPC86900
0.6689 Remote Similarity NPC197766
0.6689 Remote Similarity NPC471236
0.6667 Remote Similarity NPC113862
0.6667 Remote Similarity NPC236520
0.6667 Remote Similarity NPC294361
0.6645 Remote Similarity NPC81137
0.6643 Remote Similarity NPC105999
0.6642 Remote Similarity NPC473372
0.6641 Remote Similarity NPC471511
0.6624 Remote Similarity NPC178097
0.6619 Remote Similarity NPC150919
0.6603 Remote Similarity NPC160839
0.6597 Remote Similarity NPC213414
0.6594 Remote Similarity NPC4665
0.6552 Remote Similarity NPC3221
0.6552 Remote Similarity NPC257589
0.6552 Remote Similarity NPC53305
0.6548 Remote Similarity NPC288747
0.6544 Remote Similarity NPC297657
0.6532 Remote Similarity NPC129885
0.6525 Remote Similarity NPC299406
0.6519 Remote Similarity NPC228343
0.6519 Remote Similarity NPC254833
0.6516 Remote Similarity NPC147137
0.6515 Remote Similarity NPC8931
0.6515 Remote Similarity NPC120693
0.6515 Remote Similarity NPC261573
0.6512 Remote Similarity NPC109955
0.6507 Remote Similarity NPC92207
0.6507 Remote Similarity NPC127937
0.6503 Remote Similarity NPC137922
0.6503 Remote Similarity NPC201777
0.6503 Remote Similarity NPC40302
0.6503 Remote Similarity NPC474375
0.6503 Remote Similarity NPC472271
0.6496 Remote Similarity NPC51698
0.6483 Remote Similarity NPC471927
0.6463 Remote Similarity NPC107672
0.6458 Remote Similarity NPC159866
0.6458 Remote Similarity NPC295879
0.6458 Remote Similarity NPC25134
0.6458 Remote Similarity NPC175520
0.6458 Remote Similarity NPC64130
0.6458 Remote Similarity NPC296202
0.6458 Remote Similarity NPC97157
0.6457 Remote Similarity NPC249113
0.6454 Remote Similarity NPC63126
0.645 Remote Similarity NPC475688
0.6449 Remote Similarity NPC76400
0.6438 Remote Similarity NPC7398
0.6433 Remote Similarity NPC272868
0.6433 Remote Similarity NPC122599
0.6433 Remote Similarity NPC270848
0.6429 Remote Similarity NPC191557
0.6419 Remote Similarity NPC234175
0.6419 Remote Similarity NPC226661
0.6418 Remote Similarity NPC188677
0.6414 Remote Similarity NPC131940
0.6414 Remote Similarity NPC81149
0.6414 Remote Similarity NPC230013
0.6414 Remote Similarity NPC68350
0.6414 Remote Similarity NPC163083
0.6414 Remote Similarity NPC197576
0.6412 Remote Similarity NPC223393
0.6403 Remote Similarity NPC115803
0.6397 Remote Similarity NPC55617
0.6397 Remote Similarity NPC62258
0.6395 Remote Similarity NPC303680
0.6395 Remote Similarity NPC179777
0.6395 Remote Similarity NPC90128
0.6395 Remote Similarity NPC84076
0.6391 Remote Similarity NPC79672
0.6391 Remote Similarity NPC52087
0.6391 Remote Similarity NPC120719
0.6389 Remote Similarity NPC7830
0.6389 Remote Similarity NPC322332
0.6385 Remote Similarity NPC260000
0.638 Remote Similarity NPC294870
0.6377 Remote Similarity NPC471179
0.6376 Remote Similarity NPC304622
0.6376 Remote Similarity NPC478071
0.637 Remote Similarity NPC85565
0.637 Remote Similarity NPC236265
0.637 Remote Similarity NPC288945
0.6369 Remote Similarity NPC473941
0.6364 Remote Similarity NPC110764
0.6364 Remote Similarity NPC63317
0.6364 Remote Similarity NPC305490
0.6364 Remote Similarity NPC41232
0.6351 Remote Similarity NPC123228
0.6351 Remote Similarity NPC156539
0.6351 Remote Similarity NPC123722
0.6351 Remote Similarity NPC276466
0.6351 Remote Similarity NPC5018
0.6351 Remote Similarity NPC151167
0.635 Remote Similarity NPC226401
0.635 Remote Similarity NPC120982
0.635 Remote Similarity NPC79793
0.635 Remote Similarity NPC174096
0.635 Remote Similarity NPC147634
0.6345 Remote Similarity NPC114298
0.6336 Remote Similarity NPC280869
0.6333 Remote Similarity NPC65935
0.6333 Remote Similarity NPC215941
0.6333 Remote Similarity NPC244441
0.6333 Remote Similarity NPC123196
0.6333 Remote Similarity NPC311419
0.6333 Remote Similarity NPC11449
0.6333 Remote Similarity NPC137427
0.6333 Remote Similarity NPC244246
0.6333 Remote Similarity NPC319282
0.6333 Remote Similarity NPC275724
0.6333 Remote Similarity NPC233056
0.6331 Remote Similarity NPC317869
0.6324 Remote Similarity NPC233835
0.6319 Remote Similarity NPC226737

  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 NPC105702 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
0.6899 Remote Similarity NPD9244 Approved
0.6712 Remote Similarity NPD9718 Approved
0.6519 Remote Similarity NPD3021 Approved
0.6519 Remote Similarity NPD3022 Approved
0.625 Remote Similarity NPD3019 Approved
0.625 Remote Similarity NPD2932 Approved
0.625 Remote Similarity NPD943 Approved
0.6205 Remote Similarity NPD2296 Approved
0.6174 Remote Similarity NPD257 Approved
0.6174 Remote Similarity NPD258 Approved
0.6026 Remote Similarity NPD9569 Approved
0.6 Remote Similarity NPD8166 Discontinued
0.5973 Remote Similarity NPD4379 Clinical (unspecified phase)
0.597 Remote Similarity NPD3020 Approved
0.5957 Remote Similarity NPD228 Approved
0.5948 Remote Similarity NPD9537 Phase 1
0.5948 Remote Similarity NPD9536 Phase 1
0.5935 Remote Similarity NPD825 Approved
0.5935 Remote Similarity NPD826 Approved
0.5917 Remote Similarity NPD4288 Approved
0.5915 Remote Similarity NPD9377 Approved
0.5915 Remote Similarity NPD9379 Approved
0.5906 Remote Similarity NPD9269 Phase 2
0.5897 Remote Similarity NPD275 Approved
0.5897 Remote Similarity NPD274 Approved
0.5896 Remote Similarity NPD4010 Discontinued
0.5871 Remote Similarity NPD259 Phase 1
0.5865 Remote Similarity NPD2860 Approved
0.5865 Remote Similarity NPD2859 Approved
0.5839 Remote Similarity NPD1201 Approved
0.5817 Remote Similarity NPD9494 Approved
0.5796 Remote Similarity NPD555 Phase 2
0.5789 Remote Similarity NPD2934 Approved
0.5789 Remote Similarity NPD2933 Approved
0.5786 Remote Similarity NPD1169 Approved
0.5786 Remote Similarity NPD651 Clinical (unspecified phase)
0.5772 Remote Similarity NPD3023 Approved
0.5772 Remote Similarity NPD3026 Approved
0.5758 Remote Similarity NPD7422 Clinical (unspecified phase)
0.5753 Remote Similarity NPD405 Clinical (unspecified phase)
0.5743 Remote Similarity NPD3024 Approved
0.5743 Remote Similarity NPD3025 Approved
0.5742 Remote Similarity NPD1223 Clinical (unspecified phase)
0.5724 Remote Similarity NPD1283 Approved
0.5704 Remote Similarity NPD288 Approved
0.5697 Remote Similarity NPD1511 Approved
0.5696 Remote Similarity NPD230 Phase 1
0.5693 Remote Similarity NPD1242 Phase 1
0.5686 Remote Similarity NPD1470 Approved
0.5685 Remote Similarity NPD256 Approved
0.5685 Remote Similarity NPD255 Approved
0.5676 Remote Similarity NPD4287 Approved
0.5672 Remote Similarity NPD1432 Clinical (unspecified phase)
0.5669 Remote Similarity NPD6663 Approved
0.5664 Remote Similarity NPD9280 Clinical (unspecified phase)
0.5658 Remote Similarity NPD1755 Approved
0.5652 Remote Similarity NPD9570 Approved
0.5638 Remote Similarity NPD1651 Approved
0.5638 Remote Similarity NPD4196 Clinical (unspecified phase)
0.5638 Remote Similarity NPD9268 Approved
0.563 Remote Similarity NPD844 Approved
0.5629 Remote Similarity NPD1512 Approved
0.5625 Remote Similarity NPD1161 Approved
0.5621 Remote Similarity NPD5311 Approved
0.5621 Remote Similarity NPD5310 Approved
0.5613 Remote Similarity NPD1530 Clinical (unspecified phase)
0.5613 Remote Similarity NPD5736 Approved
0.5605 Remote Similarity NPD2028 Clinical (unspecified phase)
0.56 Remote Similarity NPD9384 Approved
0.56 Remote Similarity NPD9381 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