Structure

Physi-Chem Properties

Molecular Weight:  600.33
Volume:  608.774
LogP:  4.061
LogD:  2.669
LogS:  -3.846
# Rotatable Bonds:  12
TPSA:  131.42
# H-Bond Aceptor:  9
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.231
Synthetic Accessibility Score:  6.678
Fsp3:  0.903
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.768
MDCK Permeability:  8.384757529711351e-05
Pgp-inhibitor:  1.0
Pgp-substrate:  0.942
Human Intestinal Absorption (HIA):  0.036
20% Bioavailability (F20%):  0.007
30% Bioavailability (F30%):  0.593

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.058
Plasma Protein Binding (PPB):  94.74309539794922%
Volume Distribution (VD):  1.963
Pgp-substrate:  2.6797711849212646%

ADMET: Metabolism

CYP1A2-inhibitor:  0.02
CYP1A2-substrate:  0.111
CYP2C19-inhibitor:  0.053
CYP2C19-substrate:  0.786
CYP2C9-inhibitor:  0.252
CYP2C9-substrate:  0.039
CYP2D6-inhibitor:  0.016
CYP2D6-substrate:  0.046
CYP3A4-inhibitor:  0.798
CYP3A4-substrate:  0.567

ADMET: Excretion

Clearance (CL):  5.281
Half-life (T1/2):  0.92

ADMET: Toxicity

hERG Blockers:  0.13
Human Hepatotoxicity (H-HT):  0.938
Drug-inuced Liver Injury (DILI):  0.944
AMES Toxicity:  0.028
Rat Oral Acute Toxicity:  0.11
Maximum Recommended Daily Dose:  0.023
Skin Sensitization:  0.266
Carcinogencity:  0.046
Eye Corrosion:  0.004
Eye Irritation:  0.008
Respiratory Toxicity:  0.076

Download Data

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

  Natural Product: NPC470262

Natural Product ID:  NPC470262
Common Name*:   Klysimplexin Sulfoxide B
IUPAC Name:   n.a.
Synonyms:   Klysimplexin Sulfoxide B
Standard InCHIKey:  YAYZNOPNGRNCRX-WZEFYNERSA-N
Standard InCHI:  InChI=1S/C31H52O9S/c1-10-13-21(33)39-26-23(18(3)4)24-25(31(8,35)28(26)37-19(5)32)20-17-29(6,41(9)36)15-12-16-30(7,27(24)38-20)40-22(34)14-11-2/h18,20,23-28,35H,10-17H2,1-9H3/t20-,23-,24-,25-,26+,27-,28-,29-,30-,31+,41?/m1/s1
SMILES:  CCCC(=O)O[C@H]1[C@H](C(C)C)[C@H]2[C@H]3O[C@@H]([C@H]2[C@]([C@@H]1OC(=O)C)(C)O)C[C@](CCC[C@@]3(C)OC(=O)CCC)(C)S(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1928377
PubChem CID:   46220578
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 = 18.0 % PMID[540265]

☑ 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 NPC470262 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 NPC470261
0.8706 High Similarity NPC211049
0.8706 High Similarity NPC116320
0.8706 High Similarity NPC119922
0.866 High Similarity NPC470263
0.8372 Intermediate Similarity NPC186594
0.8353 Intermediate Similarity NPC191345
0.8353 Intermediate Similarity NPC252483
0.8353 Intermediate Similarity NPC43463
0.8222 Intermediate Similarity NPC228593
0.8222 Intermediate Similarity NPC235196
0.8182 Intermediate Similarity NPC216800
0.8118 Intermediate Similarity NPC136424
0.8023 Intermediate Similarity NPC476719
0.7865 Intermediate Similarity NPC470154
0.7826 Intermediate Similarity NPC246347
0.7789 Intermediate Similarity NPC41838
0.7778 Intermediate Similarity NPC470155
0.7778 Intermediate Similarity NPC477446
0.7778 Intermediate Similarity NPC477447
0.7742 Intermediate Similarity NPC471377
0.7717 Intermediate Similarity NPC476715
0.7717 Intermediate Similarity NPC93616
0.7667 Intermediate Similarity NPC470156
0.7634 Intermediate Similarity NPC279260
0.7558 Intermediate Similarity NPC476718
0.75 Intermediate Similarity NPC471378
0.75 Intermediate Similarity NPC312471
0.7423 Intermediate Similarity NPC122057
0.7423 Intermediate Similarity NPC312805
0.7396 Intermediate Similarity NPC291875
0.7363 Intermediate Similarity NPC472951
0.7363 Intermediate Similarity NPC472943
0.7347 Intermediate Similarity NPC475307
0.7292 Intermediate Similarity NPC476435
0.7292 Intermediate Similarity NPC75443
0.7292 Intermediate Similarity NPC92370
0.7292 Intermediate Similarity NPC470260
0.7263 Intermediate Similarity NPC477283
0.7263 Intermediate Similarity NPC476717
0.7245 Intermediate Similarity NPC91251
0.7188 Intermediate Similarity NPC110365
0.7188 Intermediate Similarity NPC213658
0.7188 Intermediate Similarity NPC45833
0.7188 Intermediate Similarity NPC44538
0.7188 Intermediate Similarity NPC62202
0.7159 Intermediate Similarity NPC123122
0.7143 Intermediate Similarity NPC470114
0.7128 Intermediate Similarity NPC239308
0.7128 Intermediate Similarity NPC476721
0.7113 Intermediate Similarity NPC476379
0.7087 Intermediate Similarity NPC272223
0.7083 Intermediate Similarity NPC475684
0.7083 Intermediate Similarity NPC215968
0.7083 Intermediate Similarity NPC155531
0.7053 Intermediate Similarity NPC18953
0.7041 Intermediate Similarity NPC161560
0.7021 Intermediate Similarity NPC154043
0.7021 Intermediate Similarity NPC60018
0.7021 Intermediate Similarity NPC202688
0.6979 Remote Similarity NPC471379
0.6979 Remote Similarity NPC477445
0.6979 Remote Similarity NPC196911
0.6979 Remote Similarity NPC266651
0.6939 Remote Similarity NPC476724
0.6939 Remote Similarity NPC476723
0.6939 Remote Similarity NPC470872
0.6939 Remote Similarity NPC471221
0.6939 Remote Similarity NPC56777
0.6939 Remote Similarity NPC201607
0.6915 Remote Similarity NPC118116
0.6907 Remote Similarity NPC471411
0.6907 Remote Similarity NPC474008
0.6907 Remote Similarity NPC471410
0.6907 Remote Similarity NPC131365
0.6893 Remote Similarity NPC111348
0.6889 Remote Similarity NPC470151
0.6842 Remote Similarity NPC477284
0.6842 Remote Similarity NPC477286
0.6842 Remote Similarity NPC286719
0.6837 Remote Similarity NPC5943
0.6813 Remote Similarity NPC472952
0.6813 Remote Similarity NPC472950
0.6809 Remote Similarity NPC474714
0.6804 Remote Similarity NPC476725
0.68 Remote Similarity NPC50443
0.68 Remote Similarity NPC18536
0.6796 Remote Similarity NPC116683
0.6796 Remote Similarity NPC235109
0.6771 Remote Similarity NPC69953
0.6771 Remote Similarity NPC5958
0.6771 Remote Similarity NPC477285
0.6771 Remote Similarity NPC127917
0.6771 Remote Similarity NPC111582
0.6768 Remote Similarity NPC309656
0.6737 Remote Similarity NPC190940
0.6737 Remote Similarity NPC475743
0.6735 Remote Similarity NPC64862
0.6735 Remote Similarity NPC103782
0.6735 Remote Similarity NPC114378
0.6733 Remote Similarity NPC473066
0.6733 Remote Similarity NPC216137
0.6723 Remote Similarity NPC198209
0.6701 Remote Similarity NPC473299
0.6701 Remote Similarity NPC477434
0.6701 Remote Similarity NPC65133
0.67 Remote Similarity NPC477440
0.67 Remote Similarity NPC477443
0.6699 Remote Similarity NPC82633
0.6698 Remote Similarity NPC98225
0.6667 Remote Similarity NPC103171
0.6667 Remote Similarity NPC122083
0.6667 Remote Similarity NPC472144
0.6667 Remote Similarity NPC256104
0.6667 Remote Similarity NPC211845
0.6667 Remote Similarity NPC182740
0.6635 Remote Similarity NPC475785
0.6635 Remote Similarity NPC163685
0.6635 Remote Similarity NPC475765
0.6634 Remote Similarity NPC477444
0.6634 Remote Similarity NPC185529
0.6634 Remote Similarity NPC477442
0.6634 Remote Similarity NPC477433
0.6634 Remote Similarity NPC472146
0.6633 Remote Similarity NPC235402
0.6633 Remote Similarity NPC478111
0.6632 Remote Similarity NPC471217
0.6632 Remote Similarity NPC186588
0.6632 Remote Similarity NPC471216
0.6604 Remote Similarity NPC188968
0.6604 Remote Similarity NPC477656
0.6598 Remote Similarity NPC29342
0.6598 Remote Similarity NPC2572
0.6598 Remote Similarity NPC15091
0.6598 Remote Similarity NPC241959
0.6574 Remote Similarity NPC61442
0.6571 Remote Similarity NPC472145
0.6569 Remote Similarity NPC219516
0.6569 Remote Similarity NPC165180
0.6566 Remote Similarity NPC321812
0.6566 Remote Similarity NPC322922
0.6566 Remote Similarity NPC268633
0.6562 Remote Similarity NPC71541
0.6562 Remote Similarity NPC77003
0.6538 Remote Similarity NPC57964
0.6538 Remote Similarity NPC94582
0.6531 Remote Similarity NPC320824
0.6526 Remote Similarity NPC477282
0.6526 Remote Similarity NPC81074
0.6526 Remote Similarity NPC477287
0.6526 Remote Similarity NPC476176
0.6522 Remote Similarity NPC55508
0.6522 Remote Similarity NPC472945
0.6522 Remote Similarity NPC166250
0.6522 Remote Similarity NPC472944
0.6509 Remote Similarity NPC253995
0.65 Remote Similarity NPC239938
0.6495 Remote Similarity NPC242771
0.6495 Remote Similarity NPC148740
0.6495 Remote Similarity NPC100366
0.6495 Remote Similarity NPC102156
0.6495 Remote Similarity NPC2096
0.6495 Remote Similarity NPC121121
0.6495 Remote Similarity NPC164289
0.6495 Remote Similarity NPC208912
0.6495 Remote Similarity NPC311642
0.6489 Remote Similarity NPC307865
0.6481 Remote Similarity NPC471254
0.6481 Remote Similarity NPC472552
0.6476 Remote Similarity NPC292718
0.6476 Remote Similarity NPC237071
0.6476 Remote Similarity NPC111834
0.6476 Remote Similarity NPC203434
0.6476 Remote Similarity NPC238796
0.6476 Remote Similarity NPC306797
0.6476 Remote Similarity NPC169270
0.6458 Remote Similarity NPC16449
0.6455 Remote Similarity NPC166079
0.6452 Remote Similarity NPC36479
0.6452 Remote Similarity NPC186851
0.6449 Remote Similarity NPC477655
0.6449 Remote Similarity NPC51579
0.6442 Remote Similarity NPC476722
0.6442 Remote Similarity NPC151214
0.6442 Remote Similarity NPC191915
0.6442 Remote Similarity NPC470424
0.6436 Remote Similarity NPC221993
0.6429 Remote Similarity NPC475820
0.6429 Remote Similarity NPC67158
0.6429 Remote Similarity NPC474346
0.6429 Remote Similarity NPC213737
0.6429 Remote Similarity NPC269684
0.6429 Remote Similarity NPC474253
0.6429 Remote Similarity NPC474284
0.6429 Remote Similarity NPC30102
0.6429 Remote Similarity NPC128816
0.6422 Remote Similarity NPC474575
0.6422 Remote Similarity NPC99510
0.6421 Remote Similarity NPC272841
0.6415 Remote Similarity NPC274793

  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 NPC470262 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
0.6742 Remote Similarity NPD7532 Clinical (unspecified phase)
0.6437 Remote Similarity NPD371 Approved
0.6429 Remote Similarity NPD3670 Clinical (unspecified phase)
0.6429 Remote Similarity NPD3669 Approved
0.6239 Remote Similarity NPD1700 Approved
0.6082 Remote Similarity NPD6114 Approved
0.6082 Remote Similarity NPD6118 Approved
0.6082 Remote Similarity NPD6697 Approved
0.6082 Remote Similarity NPD6115 Approved
0.6053 Remote Similarity NPD5345 Clinical (unspecified phase)
0.6 Remote Similarity NPD4061 Clinical (unspecified phase)
0.5979 Remote Similarity NPD6116 Phase 1
0.5948 Remote Similarity NPD5955 Clinical (unspecified phase)
0.5876 Remote Similarity NPD6117 Approved
0.5862 Remote Similarity NPD8132 Clinical (unspecified phase)
0.5804 Remote Similarity NPD5344 Discontinued
0.5789 Remote Similarity NPD8170 Clinical (unspecified phase)
0.5745 Remote Similarity NPD4267 Clinical (unspecified phase)
0.5743 Remote Similarity NPD1779 Approved
0.5743 Remote Similarity NPD1780 Approved
0.5741 Remote Similarity NPD8171 Discontinued
0.569 Remote Similarity NPD5954 Clinical (unspecified phase)
0.567 Remote Similarity NPD1811 Approved
0.567 Remote Similarity NPD1810 Approved
0.567 Remote Similarity NPD6113 Clinical (unspecified phase)
0.5667 Remote Similarity NPD8133 Approved
0.5635 Remote Similarity NPD6067 Discontinued
0.56 Remote Similarity NPD6921 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