Structure

Physi-Chem Properties

Molecular Weight:  495.23
Volume:  487.222
LogP:  3.261
LogD:  2.876
LogS:  -4.398
# Rotatable Bonds:  1
TPSA:  103.32
# H-Bond Aceptor:  8
# H-Bond Donor:  2
# Rings:  4
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.418
Synthetic Accessibility Score:  6.312
Fsp3:  0.76
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:  -4.641
MDCK Permeability:  1.8937402273877524e-05
Pgp-inhibitor:  0.54
Pgp-substrate:  0.041
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.01
30% Bioavailability (F30%):  0.981

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.104
Plasma Protein Binding (PPB):  82.34039306640625%
Volume Distribution (VD):  1.574
Pgp-substrate:  4.4929280281066895%

ADMET: Metabolism

CYP1A2-inhibitor:  0.012
CYP1A2-substrate:  0.134
CYP2C19-inhibitor:  0.743
CYP2C19-substrate:  0.768
CYP2C9-inhibitor:  0.85
CYP2C9-substrate:  0.214
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.395
CYP3A4-inhibitor:  0.887
CYP3A4-substrate:  0.488

ADMET: Excretion

Clearance (CL):  8.035
Half-life (T1/2):  0.759

ADMET: Toxicity

hERG Blockers:  0.038
Human Hepatotoxicity (H-HT):  0.9
Drug-inuced Liver Injury (DILI):  0.948
AMES Toxicity:  0.874
Rat Oral Acute Toxicity:  0.115
Maximum Recommended Daily Dose:  0.994
Skin Sensitization:  0.949
Carcinogencity:  0.081
Eye Corrosion:  0.003
Eye Irritation:  0.014
Respiratory Toxicity:  0.966

Download Data

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

  Natural Product: NPC475988

Natural Product ID:  NPC475988
Common Name*:   VMHRANMFBZFIPY-CNRKXILMSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VMHRANMFBZFIPY-CNRKXILMSA-N
Standard InCHI:  InChI=1S/C25H37NO7S/c1-15-5-8-17-12-18(13-25(29,31-17)21-14-34-23(28)26-21)30-22(27)11-16(2)7-10-20-19(9-6-15)32-24(3,4)33-20/h6,9,11,15,17-21,29H,5,7-8,10,12-14H2,1-4H3,(H,26,28)/b9-6-,16-11-/t15-,17+,18+,19-,20-,21-,25+/m0/s1
SMILES:  CC1CCC2CC(CC(O2)(C3CSC(=O)N3)O)OC(=O)C=C(CCC4C(C=C1)OC(O4)(C)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL520559
PubChem CID:   25150442
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]
NPO19376 Cacospongia mycofijiensis Species Thorectidae Eukaryota n.a. n.a. n.a. PMID[18942825]
NPO19376 Cacospongia mycofijiensis Species Thorectidae Eukaryota n.a. Tongan n.a. PMID[19877653]
NPO19376 Cacospongia mycofijiensis Species Thorectidae Eukaryota n.a. n.a. n.a. PMID[22129061]
NPO19376 Cacospongia mycofijiensis Species Thorectidae Eukaryota n.a. n.a. n.a. PMID[30371079]
NPO19376 Cacospongia mycofijiensis Species Thorectidae Eukaryota n.a. n.a. n.a. Database[UNPD]
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
NPT730 Cell Line MC-38 Mus musculus IZ = 21.0 mm PMID[463059]
NPT393 Cell Line HCT-116 Homo sapiens IC50 = 5100.0 nM PMID[463059]
NPT400 Cell Line MDA-MB-435 Homo sapiens IC50 = 7900.0 nM PMID[463059]
NPT400 Cell Line MDA-MB-435 Homo sapiens Ratio IC50 = 1.5 n.a. PMID[463059]

☑ 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 NPC475988 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
0.9528 High Similarity NPC279383
0.9429 High Similarity NPC474891
0.9346 High Similarity NPC273215
0.9346 High Similarity NPC268327
0.9346 High Similarity NPC295444
0.9333 High Similarity NPC476034
0.9333 High Similarity NPC474969
0.9327 High Similarity NPC101106
0.9327 High Similarity NPC135216
0.9238 High Similarity NPC250187
0.9151 High Similarity NPC471636
0.9151 High Similarity NPC287572
0.8981 High Similarity NPC127578
0.8762 High Similarity NPC474873
0.875 High Similarity NPC477554
0.8673 High Similarity NPC477553
0.8596 High Similarity NPC477555
0.8158 Intermediate Similarity NPC474995
0.8017 Intermediate Similarity NPC474984
0.7313 Intermediate Similarity NPC477557
0.7167 Intermediate Similarity NPC29501
0.7016 Intermediate Similarity NPC201968
0.695 Remote Similarity NPC477556
0.6942 Remote Similarity NPC122926
0.6942 Remote Similarity NPC113012
0.6855 Remote Similarity NPC50694
0.6746 Remote Similarity NPC65045
0.6642 Remote Similarity NPC477988
0.6641 Remote Similarity NPC471087
0.6641 Remote Similarity NPC326386
0.6641 Remote Similarity NPC477985
0.6638 Remote Similarity NPC475503
0.6638 Remote Similarity NPC175614
0.6636 Remote Similarity NPC471494
0.6612 Remote Similarity NPC475918
0.6609 Remote Similarity NPC256368
0.6591 Remote Similarity NPC329401
0.6591 Remote Similarity NPC477987
0.6585 Remote Similarity NPC329305
0.6577 Remote Similarity NPC311163
0.656 Remote Similarity NPC43648
0.6555 Remote Similarity NPC175531
0.6538 Remote Similarity NPC470000
0.65 Remote Similarity NPC477198
0.6493 Remote Similarity NPC471086
0.6441 Remote Similarity NPC475646
0.6441 Remote Similarity NPC4834
0.6439 Remote Similarity NPC323168
0.6439 Remote Similarity NPC111162
0.6439 Remote Similarity NPC477989
0.6439 Remote Similarity NPC293550
0.6439 Remote Similarity NPC477990
0.6404 Remote Similarity NPC133450
0.6387 Remote Similarity NPC203627
0.6379 Remote Similarity NPC238090
0.6379 Remote Similarity NPC472196
0.6379 Remote Similarity NPC472195
0.6372 Remote Similarity NPC316138
0.6372 Remote Similarity NPC313658
0.6364 Remote Similarity NPC473289
0.6357 Remote Similarity NPC469997
0.6348 Remote Similarity NPC177668
0.6348 Remote Similarity NPC118078
0.6341 Remote Similarity NPC239961
0.6333 Remote Similarity NPC474985
0.6325 Remote Similarity NPC17290
0.6325 Remote Similarity NPC35269
0.6325 Remote Similarity NPC256570
0.6325 Remote Similarity NPC23454
0.6325 Remote Similarity NPC192066
0.6325 Remote Similarity NPC70323
0.6325 Remote Similarity NPC159698
0.6325 Remote Similarity NPC3568
0.6325 Remote Similarity NPC262312
0.6303 Remote Similarity NPC52820
0.6299 Remote Similarity NPC1111
0.6299 Remote Similarity NPC261750
0.6299 Remote Similarity NPC469865
0.6296 Remote Similarity NPC474833
0.6288 Remote Similarity NPC469515
0.6279 Remote Similarity NPC30196
0.626 Remote Similarity NPC138534
0.626 Remote Similarity NPC74035
0.626 Remote Similarity NPC477000
0.626 Remote Similarity NPC477986
0.626 Remote Similarity NPC75523
0.626 Remote Similarity NPC477001
0.625 Remote Similarity NPC193471
0.625 Remote Similarity NPC329919
0.625 Remote Similarity NPC477793
0.625 Remote Similarity NPC266718
0.625 Remote Similarity NPC130124
0.6241 Remote Similarity NPC230889
0.6239 Remote Similarity NPC471483
0.6239 Remote Similarity NPC156553
0.6239 Remote Similarity NPC139712
0.6231 Remote Similarity NPC6531
0.623 Remote Similarity NPC474244
0.6225 Remote Similarity NPC473208
0.622 Remote Similarity NPC47857
0.622 Remote Similarity NPC181510
0.622 Remote Similarity NPC168758
0.6218 Remote Similarity NPC173329
0.6218 Remote Similarity NPC45313
0.6218 Remote Similarity NPC183449
0.6218 Remote Similarity NPC288350
0.6218 Remote Similarity NPC197294
0.6218 Remote Similarity NPC8098
0.621 Remote Similarity NPC154601
0.621 Remote Similarity NPC201128
0.6207 Remote Similarity NPC74672
0.6207 Remote Similarity NPC202886
0.6207 Remote Similarity NPC242503
0.6207 Remote Similarity NPC43074
0.6207 Remote Similarity NPC471569
0.6207 Remote Similarity NPC209047
0.6207 Remote Similarity NPC139782
0.6194 Remote Similarity NPC315783
0.6194 Remote Similarity NPC316133
0.6194 Remote Similarity NPC318445
0.6194 Remote Similarity NPC163365
0.619 Remote Similarity NPC24389
0.619 Remote Similarity NPC473578
0.619 Remote Similarity NPC133625
0.6183 Remote Similarity NPC106791
0.6183 Remote Similarity NPC201889
0.6179 Remote Similarity NPC55336
0.6179 Remote Similarity NPC472747
0.6179 Remote Similarity NPC472750
0.6172 Remote Similarity NPC60432
0.6167 Remote Similarity NPC476344
0.6165 Remote Similarity NPC23963
0.6161 Remote Similarity NPC2379
0.6161 Remote Similarity NPC106912
0.6161 Remote Similarity NPC263087
0.6161 Remote Similarity NPC31019
0.6161 Remote Similarity NPC27314
0.6154 Remote Similarity NPC309898
0.6154 Remote Similarity NPC469410
0.6154 Remote Similarity NPC61894
0.6154 Remote Similarity NPC15851
0.6154 Remote Similarity NPC182632
0.6154 Remote Similarity NPC282705
0.6154 Remote Similarity NPC475125
0.6154 Remote Similarity NPC473581
0.6154 Remote Similarity NPC473604
0.6154 Remote Similarity NPC475603
0.6154 Remote Similarity NPC111567
0.6154 Remote Similarity NPC473950
0.6154 Remote Similarity NPC263545
0.6154 Remote Similarity NPC186840
0.6148 Remote Similarity NPC198992
0.6148 Remote Similarity NPC469494
0.6136 Remote Similarity NPC67917
0.6136 Remote Similarity NPC314268
0.6136 Remote Similarity NPC477515
0.6136 Remote Similarity NPC313802
0.6134 Remote Similarity NPC150041
0.6129 Remote Similarity NPC14537
0.6129 Remote Similarity NPC472748
0.6129 Remote Similarity NPC64168
0.6126 Remote Similarity NPC471552
0.6126 Remote Similarity NPC473339
0.6121 Remote Similarity NPC477748
0.6119 Remote Similarity NPC469943
0.6116 Remote Similarity NPC270813
0.6115 Remote Similarity NPC316401
0.6111 Remote Similarity NPC469880
0.6111 Remote Similarity NPC475150
0.6106 Remote Similarity NPC78673
0.6106 Remote Similarity NPC160517
0.6106 Remote Similarity NPC186155
0.6094 Remote Similarity NPC316984
0.6094 Remote Similarity NPC30911
0.609 Remote Similarity NPC230849
0.6087 Remote Similarity NPC199382
0.6083 Remote Similarity NPC189629
0.608 Remote Similarity NPC472751
0.608 Remote Similarity NPC472433
0.608 Remote Similarity NPC473252
0.608 Remote Similarity NPC271269
0.608 Remote Similarity NPC93179
0.608 Remote Similarity NPC472749
0.6068 Remote Similarity NPC475995
0.6068 Remote Similarity NPC477865
0.6068 Remote Similarity NPC3952
0.6068 Remote Similarity NPC474098
0.6068 Remote Similarity NPC477866
0.6063 Remote Similarity NPC206618
0.6061 Remote Similarity NPC315974
0.6061 Remote Similarity NPC235625
0.6061 Remote Similarity NPC284656
0.6061 Remote Similarity NPC9714
0.6058 Remote Similarity NPC314282
0.6058 Remote Similarity NPC204556
0.605 Remote Similarity NPC158445
0.605 Remote Similarity NPC157353
0.605 Remote Similarity NPC282088
0.605 Remote Similarity NPC156782
0.605 Remote Similarity NPC54961

  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 NPC475988 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
0.9327 High Similarity NPD4211 Phase 1
0.7016 Intermediate Similarity NPD7505 Discontinued
0.6528 Remote Similarity NPD7625 Phase 1
0.6356 Remote Similarity NPD4228 Discovery
0.627 Remote Similarity NPD6421 Discontinued
0.6207 Remote Similarity NPD8522 Clinical (unspecified phase)
0.6194 Remote Similarity NPD7829 Approved
0.6194 Remote Similarity NPD7642 Approved
0.6194 Remote Similarity NPD7830 Approved
0.619 Remote Similarity NPD6413 Approved
0.6183 Remote Similarity NPD7641 Discontinued
0.6116 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6103 Remote Similarity NPD8451 Approved
0.6094 Remote Similarity NPD2204 Approved
0.6068 Remote Similarity NPD46 Approved
0.6068 Remote Similarity NPD6698 Approved
0.6058 Remote Similarity NPD8448 Approved
0.6048 Remote Similarity NPD1407 Approved
0.6045 Remote Similarity NPD8444 Approved
0.6043 Remote Similarity NPD8392 Approved
0.6043 Remote Similarity NPD8390 Approved
0.6043 Remote Similarity NPD8391 Approved
0.6016 Remote Similarity NPD6420 Discontinued
0.5985 Remote Similarity NPD7500 Approved
0.5966 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5932 Remote Similarity NPD7838 Discovery
0.5932 Remote Similarity NPD6095 Approved
0.5932 Remote Similarity NPD6094 Approved
0.5929 Remote Similarity NPD6914 Discontinued
0.5912 Remote Similarity NPD8341 Approved
0.5912 Remote Similarity NPD8342 Approved
0.5912 Remote Similarity NPD8340 Approved
0.5912 Remote Similarity NPD8299 Approved
0.5896 Remote Similarity NPD2495 Phase 3
0.5859 Remote Similarity NPD6686 Approved
0.5846 Remote Similarity NPD7116 Clinical (unspecified phase)
0.5826 Remote Similarity NPD6400 Clinical (unspecified phase)
0.582 Remote Similarity NPD3190 Approved
0.582 Remote Similarity NPD7839 Suspended
0.582 Remote Similarity NPD3189 Approved
0.582 Remote Similarity NPD3191 Approved
0.5766 Remote Similarity NPD8080 Discontinued
0.5764 Remote Similarity NPD8415 Approved
0.5755 Remote Similarity NPD8273 Phase 1
0.5746 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5725 Remote Similarity NPD1719 Phase 1
0.5725 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5724 Remote Similarity NPD7274 Clinical (unspecified phase)
0.5714 Remote Similarity NPD8074 Phase 3
0.5703 Remote Similarity NPD5357 Phase 1
0.5693 Remote Similarity NPD7739 Clinical (unspecified phase)
0.5683 Remote Similarity NPD4480 Approved
0.5674 Remote Similarity NPD8337 Approved
0.5674 Remote Similarity NPD8336 Approved
0.5669 Remote Similarity NPD2258 Approved
0.5669 Remote Similarity NPD2259 Approved
0.5662 Remote Similarity NPD7518 Approved
0.5662 Remote Similarity NPD7517 Approved
0.5662 Remote Similarity NPD7519 Approved
0.5652 Remote Similarity NPD7623 Phase 3
0.5652 Remote Similarity NPD7624 Clinical (unspecified phase)
0.5635 Remote Similarity NPD5344 Discontinued
0.5625 Remote Similarity NPD8338 Approved
0.562 Remote Similarity NPD4810 Clinical (unspecified phase)
0.5616 Remote Similarity NPD8387 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