Structure

Physi-Chem Properties

Molecular Weight:  498.3
Volume:  515.856
LogP:  4.164
LogD:  3.171
LogS:  -4.451
# Rotatable Bonds:  8
TPSA:  84.89
# H-Bond Aceptor:  6
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.37
Synthetic Accessibility Score:  6.469
Fsp3:  0.926
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.767
MDCK Permeability:  5.188139039091766e-05
Pgp-inhibitor:  0.998
Pgp-substrate:  0.252
Human Intestinal Absorption (HIA):  0.013
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.25

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.05
Plasma Protein Binding (PPB):  97.01321411132812%
Volume Distribution (VD):  1.642
Pgp-substrate:  2.525250196456909%

ADMET: Metabolism

CYP1A2-inhibitor:  0.025
CYP1A2-substrate:  0.295
CYP2C19-inhibitor:  0.143
CYP2C19-substrate:  0.928
CYP2C9-inhibitor:  0.548
CYP2C9-substrate:  0.036
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.065
CYP3A4-inhibitor:  0.836
CYP3A4-substrate:  0.713

ADMET: Excretion

Clearance (CL):  5.71
Half-life (T1/2):  0.673

ADMET: Toxicity

hERG Blockers:  0.078
Human Hepatotoxicity (H-HT):  0.829
Drug-inuced Liver Injury (DILI):  0.93
AMES Toxicity:  0.014
Rat Oral Acute Toxicity:  0.044
Maximum Recommended Daily Dose:  0.013
Skin Sensitization:  0.183
Carcinogencity:  0.106
Eye Corrosion:  0.017
Eye Irritation:  0.021
Respiratory Toxicity:  0.113

Download Data

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

  Natural Product: NPC470261

Natural Product ID:  NPC470261
Common Name*:   Klysimplexin Sulfoxide A
IUPAC Name:   n.a.
Synonyms:   Klysimplexin Sulfoxide A
Standard InCHIKey:  UECSYUNUKGMBSJ-JCFNUAFHSA-N
Standard InCHI:  InChI=1S/C27H46O6S/c1-9-11-21(29)33-27(7)14-10-13-25(5,34(8)30)16-20-23-22(24(27)31-20)19(17(2)3)12-15-26(23,6)32-18(4)28/h17,19-20,22-24H,9-16H2,1-8H3/t19-,20-,22-,23-,24-,25-,26-,27-,34?/m1/s1
SMILES:  CCCC(=O)OC1(CCCC(CC2C3C(C1O2)C(CCC3(C)OC(=O)C)C(C)C)(C)S(=O)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1928376
PubChem CID:   46220577
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0002916] Eunicellane and asbestinane diterpenoids

*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
NPO32470 octocorallia sp. Species n.a. Eukaryota n.a. n.a. n.a. PMID[21970540]

☑ 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
NPT113 Cell Line RAW264.7 Mus musculus Activity = 8.8 % PMID[532909]

☑ 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 NPC470261 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
0.9167 High Similarity NPC470262
0.8228 Intermediate Similarity NPC476718
0.8171 Intermediate Similarity NPC252483
0.8171 Intermediate Similarity NPC191345
0.7938 Intermediate Similarity NPC470263
0.7927 Intermediate Similarity NPC136424
0.7882 Intermediate Similarity NPC211049
0.7882 Intermediate Similarity NPC119922
0.7882 Intermediate Similarity NPC116320
0.7831 Intermediate Similarity NPC476719
0.7778 Intermediate Similarity NPC123122
0.7738 Intermediate Similarity NPC43463
0.7701 Intermediate Similarity NPC476721
0.7558 Intermediate Similarity NPC186594
0.7528 Intermediate Similarity NPC476715
0.7444 Intermediate Similarity NPC235196
0.7444 Intermediate Similarity NPC228593
0.7386 Intermediate Similarity NPC216800
0.7303 Intermediate Similarity NPC127917
0.7283 Intermediate Similarity NPC92370
0.7222 Intermediate Similarity NPC65133
0.7204 Intermediate Similarity NPC291875
0.7159 Intermediate Similarity NPC472943
0.7159 Intermediate Similarity NPC472951
0.7159 Intermediate Similarity NPC471216
0.7159 Intermediate Similarity NPC471217
0.7143 Intermediate Similarity NPC93616
0.7143 Intermediate Similarity NPC476725
0.7079 Intermediate Similarity NPC470154
0.7079 Intermediate Similarity NPC71541
0.7065 Intermediate Similarity NPC279260
0.7065 Intermediate Similarity NPC474008
0.7065 Intermediate Similarity NPC476717
0.7065 Intermediate Similarity NPC475684
0.7065 Intermediate Similarity NPC246347
0.7059 Intermediate Similarity NPC55508
0.7053 Intermediate Similarity NPC312805
0.7053 Intermediate Similarity NPC41838
0.7053 Intermediate Similarity NPC165180
0.7045 Intermediate Similarity NPC477287
0.7 Intermediate Similarity NPC477447
0.7 Intermediate Similarity NPC470155
0.7 Intermediate Similarity NPC477446
0.7 Intermediate Similarity NPC477284
0.6989 Remote Similarity NPC44538
0.6989 Remote Similarity NPC471377
0.6947 Remote Similarity NPC471378
0.6947 Remote Similarity NPC312471
0.6923 Remote Similarity NPC239308
0.6915 Remote Similarity NPC75443
0.6915 Remote Similarity NPC476724
0.6915 Remote Similarity NPC476723
0.6915 Remote Similarity NPC221993
0.6915 Remote Similarity NPC471221
0.6915 Remote Similarity NPC470260
0.6907 Remote Similarity NPC476722
0.6889 Remote Similarity NPC470156
0.6882 Remote Similarity NPC214315
0.6875 Remote Similarity NPC122057
0.6848 Remote Similarity NPC18953
0.6842 Remote Similarity NPC161560
0.6778 Remote Similarity NPC125366
0.6778 Remote Similarity NPC134227
0.6774 Remote Similarity NPC196911
0.6774 Remote Similarity NPC471379
0.6744 Remote Similarity NPC109510
0.6742 Remote Similarity NPC264610
0.6739 Remote Similarity NPC5958
0.6737 Remote Similarity NPC476435
0.6735 Remote Similarity NPC476716
0.6703 Remote Similarity NPC118116
0.6702 Remote Similarity NPC477441
0.6702 Remote Similarity NPC215968
0.6702 Remote Similarity NPC477283
0.6702 Remote Similarity NPC471411
0.6702 Remote Similarity NPC471410
0.6702 Remote Similarity NPC155531
0.6701 Remote Similarity NPC216137
0.6701 Remote Similarity NPC91251
0.67 Remote Similarity NPC111348
0.6667 Remote Similarity NPC473299
0.6667 Remote Similarity NPC477434
0.6633 Remote Similarity NPC474379
0.6633 Remote Similarity NPC475307
0.6632 Remote Similarity NPC110365
0.6632 Remote Similarity NPC62202
0.6632 Remote Similarity NPC213658
0.6632 Remote Similarity NPC45833
0.663 Remote Similarity NPC477286
0.663 Remote Similarity NPC286719
0.6629 Remote Similarity NPC143250
0.6598 Remote Similarity NPC470114
0.6596 Remote Similarity NPC477445
0.6593 Remote Similarity NPC474714
0.6593 Remote Similarity NPC475456
0.6593 Remote Similarity NPC60568
0.6591 Remote Similarity NPC472950
0.6591 Remote Similarity NPC472952
0.6562 Remote Similarity NPC56777
0.6562 Remote Similarity NPC476379
0.6562 Remote Similarity NPC470872
0.6562 Remote Similarity NPC201607
0.6562 Remote Similarity NPC309656
0.6559 Remote Similarity NPC111582
0.6559 Remote Similarity NPC477285
0.6526 Remote Similarity NPC114378
0.6526 Remote Similarity NPC322922
0.6526 Remote Similarity NPC103782
0.6526 Remote Similarity NPC321812
0.6522 Remote Similarity NPC77003
0.6522 Remote Similarity NPC190940
0.6522 Remote Similarity NPC475743
0.6495 Remote Similarity NPC477443
0.6495 Remote Similarity NPC477440
0.6484 Remote Similarity NPC476176
0.6452 Remote Similarity NPC208912
0.6452 Remote Similarity NPC202688
0.6452 Remote Similarity NPC2096
0.6452 Remote Similarity NPC154043
0.6452 Remote Similarity NPC103171
0.6452 Remote Similarity NPC60018
0.6444 Remote Similarity NPC307865
0.6436 Remote Similarity NPC116683
0.6436 Remote Similarity NPC235109
0.6429 Remote Similarity NPC477444
0.6429 Remote Similarity NPC50443
0.6429 Remote Similarity NPC477442
0.6429 Remote Similarity NPC18536
0.6429 Remote Similarity NPC477433
0.6421 Remote Similarity NPC266651
0.6421 Remote Similarity NPC235402
0.642 Remote Similarity NPC204173
0.6408 Remote Similarity NPC272223
0.6404 Remote Similarity NPC186851
0.64 Remote Similarity NPC477495
0.6383 Remote Similarity NPC29342
0.6383 Remote Similarity NPC2572
0.6383 Remote Similarity NPC213737
0.6383 Remote Similarity NPC474253
0.6383 Remote Similarity NPC69953
0.6383 Remote Similarity NPC15091
0.6383 Remote Similarity NPC474346
0.6383 Remote Similarity NPC475820
0.6383 Remote Similarity NPC474284
0.6373 Remote Similarity NPC266417
0.6364 Remote Similarity NPC474755
0.6364 Remote Similarity NPC473066
0.6364 Remote Similarity NPC8729
0.6354 Remote Similarity NPC131365
0.6354 Remote Similarity NPC64862
0.6353 Remote Similarity NPC476928
0.6344 Remote Similarity NPC329490
0.6344 Remote Similarity NPC73515
0.6344 Remote Similarity NPC328639
0.6337 Remote Similarity NPC82633
0.6337 Remote Similarity NPC476720
0.6333 Remote Similarity NPC474020
0.6304 Remote Similarity NPC73013
0.63 Remote Similarity NPC35164
0.63 Remote Similarity NPC122083
0.63 Remote Similarity NPC211845
0.63 Remote Similarity NPC182740
0.63 Remote Similarity NPC256104
0.6292 Remote Similarity NPC472945
0.6292 Remote Similarity NPC470151
0.6292 Remote Similarity NPC472944
0.6289 Remote Similarity NPC5943
0.6277 Remote Similarity NPC311642
0.6277 Remote Similarity NPC242771
0.6277 Remote Similarity NPC13494
0.6277 Remote Similarity NPC100366
0.6277 Remote Similarity NPC148740
0.6277 Remote Similarity NPC164289
0.6277 Remote Similarity NPC102156
0.6275 Remote Similarity NPC163685
0.6275 Remote Similarity NPC475765
0.6275 Remote Similarity NPC475785
0.6271 Remote Similarity NPC198209
0.6264 Remote Similarity NPC471151
0.6264 Remote Similarity NPC212453
0.6263 Remote Similarity NPC185529
0.6263 Remote Similarity NPC472146
0.625 Remote Similarity NPC478111
0.6238 Remote Similarity NPC470424
0.6235 Remote Similarity NPC84562
0.6222 Remote Similarity NPC36479
0.6222 Remote Similarity NPC478105
0.6211 Remote Similarity NPC67158
0.6211 Remote Similarity NPC30102
0.6211 Remote Similarity NPC128816
0.62 Remote Similarity NPC208839
0.62 Remote Similarity NPC475878
0.6196 Remote Similarity NPC471045
0.6176 Remote Similarity NPC21897
0.617 Remote Similarity NPC30443
0.617 Remote Similarity NPC260977
0.617 Remote Similarity NPC476494
0.617 Remote Similarity NPC45256
0.617 Remote Similarity NPC285480
0.6162 Remote Similarity NPC67653

  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 NPC470261 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
0.6211 Remote Similarity NPD3669 Approved
0.6211 Remote Similarity NPD3670 Clinical (unspecified phase)
0.617 Remote Similarity NPD1779 Approved
0.617 Remote Similarity NPD1780 Approved
0.6022 Remote Similarity NPD6114 Approved
0.6022 Remote Similarity NPD6115 Approved
0.6022 Remote Similarity NPD6697 Approved
0.6022 Remote Similarity NPD6118 Approved
0.5955 Remote Similarity NPD2687 Approved
0.5955 Remote Similarity NPD2686 Approved
0.5955 Remote Similarity NPD7532 Clinical (unspecified phase)
0.5955 Remote Similarity NPD2254 Approved
0.5914 Remote Similarity NPD6116 Phase 1
0.5888 Remote Similarity NPD1700 Approved
0.5854 Remote Similarity NPD4279 Approved
0.5814 Remote Similarity NPD371 Approved
0.5806 Remote Similarity NPD6117 Approved
0.5714 Remote Similarity NPD4280 Approved
0.5714 Remote Similarity NPD5777 Approved
0.5625 Remote Similarity NPD5954 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