Structure

Physi-Chem Properties

Molecular Weight:  843.68
Volume:  923.833
LogP:  9.486
LogD:  4.914
LogS:  -1.576
# Rotatable Bonds:  42
TPSA:  189.17
# H-Bond Aceptor:  11
# H-Bond Donor:  8
# Rings:  1
# Heavy Atoms:  11

MedChem Properties

QED Drug-Likeness Score:  0.022
Synthetic Accessibility Score:  4.924
Fsp3:  0.938
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  2
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.554
MDCK Permeability:  2.5854926661850186e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.009
Human Intestinal Absorption (HIA):  0.821
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.002
Plasma Protein Binding (PPB):  103.37810516357422%
Volume Distribution (VD):  0.884
Pgp-substrate:  1.256333351135254%

ADMET: Metabolism

CYP1A2-inhibitor:  0.013
CYP1A2-substrate:  0.1
CYP2C19-inhibitor:  0.074
CYP2C19-substrate:  0.033
CYP2C9-inhibitor:  0.041
CYP2C9-substrate:  0.993
CYP2D6-inhibitor:  0.013
CYP2D6-substrate:  0.01
CYP3A4-inhibitor:  0.142
CYP3A4-substrate:  0.003

ADMET: Excretion

Clearance (CL):  2.793
Half-life (T1/2):  0.521

ADMET: Toxicity

hERG Blockers:  0.859
Human Hepatotoxicity (H-HT):  0.041
Drug-inuced Liver Injury (DILI):  0.007
AMES Toxicity:  0.163
Rat Oral Acute Toxicity:  0.003
Maximum Recommended Daily Dose:  0.004
Skin Sensitization:  0.974
Carcinogencity:  0.008
Eye Corrosion:  0.003
Eye Irritation:  0.013
Respiratory Toxicity:  0.705

Download Data

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

  Natural Product: NPC475603

Natural Product ID:  NPC475603
Common Name*:   Sumatranoside
IUPAC Name:   (2S)-N-[(Z,3S,4R)-3,4-dihydroxy-1-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoctadec-9-en-2-yl]-2-hydroxytetracosanamide
Synonyms:   sumatranoside
Standard InCHIKey:  AQVPIVKUWUUSPC-XKIDKVJTSA-N
Standard InCHI:  InChI=1S/C48H93NO10/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-26-28-30-32-34-36-41(52)47(57)49-39(38-58-48-46(56)45(55)44(54)42(37-50)59-48)43(53)40(51)35-33-31-29-27-25-16-14-12-10-8-6-4-2/h25,27,39-46,48,50-56H,3-24,26,28-38H2,1-2H3,(H,49,57)/b27-25-/t39?,40-,41+,42-,43+,44-,45+,46-,48-/m1/s1
SMILES:  CCCCCCCCCCCCCCCCCCCCCCC(C(=O)NC(COC1C(C(C(C(O1)CO)O)O)O)C(C(CCCCC=CCCCCCCCC)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL509082
PubChem CID:   44575768
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000257] Sphingolipids
        • [CHEMONTID:0003258] Glycosphingolipids

*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
NPO21558 Ormosia sumatrana Species Fabaceae Eukaryota leaves n.a. n.a. PMID[15568789]
NPO21558 Ormosia sumatrana Species Fabaceae 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
NPT2 Others Unspecified IC50 = 30000.0 nM PMID[575677]

☑ 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 NPC475603 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
1.0 High Similarity NPC61894
0.9318 High Similarity NPC473581
0.9318 High Similarity NPC309898
0.9318 High Similarity NPC263545
0.9318 High Similarity NPC473950
0.9318 High Similarity NPC186840
0.9318 High Similarity NPC473604
0.9318 High Similarity NPC15851
0.9318 High Similarity NPC111567
0.9318 High Similarity NPC475125
0.9205 High Similarity NPC139782
0.9205 High Similarity NPC74672
0.9205 High Similarity NPC43074
0.9205 High Similarity NPC242503
0.9205 High Similarity NPC209047
0.9111 High Similarity NPC157353
0.9111 High Similarity NPC3568
0.9111 High Similarity NPC282088
0.9111 High Similarity NPC256570
0.9111 High Similarity NPC54961
0.9111 High Similarity NPC158445
0.9111 High Similarity NPC192066
0.9111 High Similarity NPC17290
0.9111 High Similarity NPC156782
0.9101 High Similarity NPC182632
0.9101 High Similarity NPC282705
0.9043 High Similarity NPC477198
0.8913 High Similarity NPC8098
0.8913 High Similarity NPC183449
0.8913 High Similarity NPC197294
0.8901 High Similarity NPC70323
0.8901 High Similarity NPC35269
0.8901 High Similarity NPC262312
0.8901 High Similarity NPC23454
0.871 High Similarity NPC45313
0.8384 Intermediate Similarity NPC475918
0.8118 Intermediate Similarity NPC264417
0.8118 Intermediate Similarity NPC217095
0.8111 Intermediate Similarity NPC476523
0.802 Intermediate Similarity NPC201128
0.7684 Intermediate Similarity NPC39290
0.7684 Intermediate Similarity NPC159369
0.764 Intermediate Similarity NPC474833
0.7576 Intermediate Similarity NPC189629
0.7525 Intermediate Similarity NPC225978
0.7525 Intermediate Similarity NPC255175
0.7525 Intermediate Similarity NPC206711
0.7525 Intermediate Similarity NPC271207
0.7471 Intermediate Similarity NPC55652
0.74 Intermediate Similarity NPC475503
0.7396 Intermediate Similarity NPC470284
0.7386 Intermediate Similarity NPC288086
0.734 Intermediate Similarity NPC477199
0.7327 Intermediate Similarity NPC475646
0.7253 Intermediate Similarity NPC316807
0.7238 Intermediate Similarity NPC74035
0.7172 Intermediate Similarity NPC208537
0.7172 Intermediate Similarity NPC270005
0.7053 Intermediate Similarity NPC228638
0.703 Intermediate Similarity NPC470283
0.7021 Intermediate Similarity NPC21693
0.7021 Intermediate Similarity NPC236649
0.7 Intermediate Similarity NPC29501
0.6983 Remote Similarity NPC469943
0.6947 Remote Similarity NPC474312
0.6932 Remote Similarity NPC327753
0.6932 Remote Similarity NPC103712
0.6932 Remote Similarity NPC223174
0.6932 Remote Similarity NPC291196
0.6932 Remote Similarity NPC327486
0.6923 Remote Similarity NPC3094
0.6915 Remote Similarity NPC471420
0.6875 Remote Similarity NPC156089
0.6875 Remote Similarity NPC470313
0.6875 Remote Similarity NPC473500
0.6875 Remote Similarity NPC38295
0.6822 Remote Similarity NPC55336
0.6786 Remote Similarity NPC314306
0.6774 Remote Similarity NPC110813
0.6744 Remote Similarity NPC13143
0.6744 Remote Similarity NPC294813
0.6706 Remote Similarity NPC145627
0.6702 Remote Similarity NPC133377
0.6702 Remote Similarity NPC150557
0.6667 Remote Similarity NPC474078
0.6667 Remote Similarity NPC475472
0.6667 Remote Similarity NPC473578
0.6667 Remote Similarity NPC469469
0.6637 Remote Similarity NPC261750
0.6637 Remote Similarity NPC1111
0.6636 Remote Similarity NPC315426
0.6633 Remote Similarity NPC192025
0.6633 Remote Similarity NPC253975
0.6633 Remote Similarity NPC125253
0.6629 Remote Similarity NPC474812
0.6613 Remote Similarity NPC119794
0.6613 Remote Similarity NPC73829
0.66 Remote Similarity NPC470282
0.6577 Remote Similarity NPC475150
0.6562 Remote Similarity NPC79367
0.656 Remote Similarity NPC76999
0.6532 Remote Similarity NPC139585
0.6508 Remote Similarity NPC75318
0.6508 Remote Similarity NPC280941
0.6508 Remote Similarity NPC235772
0.6504 Remote Similarity NPC313962
0.65 Remote Similarity NPC208473
0.6491 Remote Similarity NPC469865
0.6491 Remote Similarity NPC60432
0.6481 Remote Similarity NPC42320
0.6481 Remote Similarity NPC188453
0.6476 Remote Similarity NPC330590
0.6471 Remote Similarity NPC329003
0.6471 Remote Similarity NPC325550
0.6471 Remote Similarity NPC326524
0.6457 Remote Similarity NPC145899
0.6452 Remote Similarity NPC472173
0.6452 Remote Similarity NPC472174
0.6446 Remote Similarity NPC313342
0.6446 Remote Similarity NPC204639
0.6446 Remote Similarity NPC313333
0.6446 Remote Similarity NPC314451
0.6446 Remote Similarity NPC314512
0.6441 Remote Similarity NPC314268
0.6441 Remote Similarity NPC477515
0.6441 Remote Similarity NPC313802
0.6441 Remote Similarity NPC67917
0.6423 Remote Similarity NPC329919
0.6423 Remote Similarity NPC477793
0.6415 Remote Similarity NPC175614
0.641 Remote Similarity NPC6531
0.64 Remote Similarity NPC83839
0.6392 Remote Similarity NPC100697
0.6392 Remote Similarity NPC163362
0.6392 Remote Similarity NPC127295
0.6383 Remote Similarity NPC51055
0.6383 Remote Similarity NPC62293
0.6383 Remote Similarity NPC140327
0.6383 Remote Similarity NPC212008
0.6364 Remote Similarity NPC314629
0.6357 Remote Similarity NPC200788
0.6357 Remote Similarity NPC243680
0.6353 Remote Similarity NPC321030
0.6348 Remote Similarity NPC279383
0.6344 Remote Similarity NPC132938
0.6341 Remote Similarity NPC314282
0.6337 Remote Similarity NPC306838
0.6333 Remote Similarity NPC195165
0.6327 Remote Similarity NPC271772
0.6327 Remote Similarity NPC280367
0.6327 Remote Similarity NPC36927
0.6327 Remote Similarity NPC82799
0.6325 Remote Similarity NPC313813
0.6325 Remote Similarity NPC30196
0.6316 Remote Similarity NPC229655
0.6316 Remote Similarity NPC326661
0.6308 Remote Similarity NPC302276
0.6308 Remote Similarity NPC180770
0.63 Remote Similarity NPC473308
0.6293 Remote Similarity NPC241597
0.6289 Remote Similarity NPC318258
0.6281 Remote Similarity NPC273185
0.6263 Remote Similarity NPC165119
0.6263 Remote Similarity NPC20072
0.6263 Remote Similarity NPC251026
0.626 Remote Similarity NPC315058
0.626 Remote Similarity NPC82931
0.626 Remote Similarity NPC172365
0.626 Remote Similarity NPC210729
0.625 Remote Similarity NPC477866
0.625 Remote Similarity NPC477865
0.625 Remote Similarity NPC277570
0.624 Remote Similarity NPC316205
0.624 Remote Similarity NPC315387
0.6238 Remote Similarity NPC73166
0.623 Remote Similarity NPC315783
0.622 Remote Similarity NPC314361
0.6214 Remote Similarity NPC292345
0.6212 Remote Similarity NPC162910
0.6207 Remote Similarity NPC268327
0.6207 Remote Similarity NPC477763
0.6207 Remote Similarity NPC477757
0.6207 Remote Similarity NPC477753
0.6207 Remote Similarity NPC477750
0.6207 Remote Similarity NPC295444
0.6207 Remote Similarity NPC477762
0.6207 Remote Similarity NPC273215
0.6207 Remote Similarity NPC477755
0.62 Remote Similarity NPC142111
0.62 Remote Similarity NPC473315
0.619 Remote Similarity NPC472197
0.619 Remote Similarity NPC472199
0.6176 Remote Similarity NPC470836
0.6172 Remote Similarity NPC78189
0.6172 Remote Similarity NPC477072
0.617 Remote Similarity NPC314678
0.617 Remote Similarity NPC305223
0.6165 Remote Similarity NPC475584
0.6165 Remote Similarity NPC475394
0.6165 Remote Similarity NPC475152

  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 NPC475603 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
0.9205 High Similarity NPD8522 Clinical (unspecified phase)
0.6981 Remote Similarity NPD1407 Approved
0.6932 Remote Similarity NPD9445 Approved
0.6909 Remote Similarity NPD6421 Discontinued
0.6838 Remote Similarity NPD6436 Phase 3
0.6786 Remote Similarity NPD6429 Approved
0.6786 Remote Similarity NPD6430 Approved
0.6634 Remote Similarity NPD3716 Discontinued
0.6571 Remote Similarity NPD6428 Approved
0.6496 Remote Similarity NPD7641 Discontinued
0.6476 Remote Similarity NPD5381 Approved
0.6476 Remote Similarity NPD5377 Approved
0.6476 Remote Similarity NPD5378 Approved
0.6446 Remote Similarity NPD8341 Approved
0.6446 Remote Similarity NPD8299 Approved
0.6446 Remote Similarity NPD8340 Approved
0.6446 Remote Similarity NPD8342 Approved
0.6436 Remote Similarity NPD4759 Clinical (unspecified phase)
0.6396 Remote Similarity NPD5357 Phase 1
0.6393 Remote Similarity NPD8451 Approved
0.6364 Remote Similarity NPD8045 Clinical (unspecified phase)
0.6341 Remote Similarity NPD8448 Approved
0.6333 Remote Similarity NPD8444 Approved
0.6293 Remote Similarity NPD3731 Phase 3
0.6283 Remote Similarity NPD8174 Phase 2
0.623 Remote Similarity NPD7829 Approved
0.623 Remote Similarity NPD7830 Approved
0.6214 Remote Similarity NPD618 Clinical (unspecified phase)
0.619 Remote Similarity NPD8392 Approved
0.619 Remote Similarity NPD8391 Approved
0.619 Remote Similarity NPD8390 Approved
0.6186 Remote Similarity NPD4831 Approved
0.6186 Remote Similarity NPD4832 Approved
0.6186 Remote Similarity NPD4830 Approved
0.6134 Remote Similarity NPD8137 Clinical (unspecified phase)
0.6132 Remote Similarity NPD1446 Phase 3
0.6132 Remote Similarity NPD1447 Phase 3
0.6106 Remote Similarity NPD5376 Approved
0.6098 Remote Similarity NPD7642 Approved
0.6087 Remote Similarity NPD6941 Approved
0.6082 Remote Similarity NPD9434 Approved
0.6082 Remote Similarity NPD9435 Approved
0.6019 Remote Similarity NPD7844 Discontinued
0.6 Remote Similarity NPD2255 Approved
0.5982 Remote Similarity NPD7141 Clinical (unspecified phase)
0.5982 Remote Similarity NPD7140 Approved
0.5982 Remote Similarity NPD7139 Approved
0.5965 Remote Similarity NPD4211 Phase 1
0.5948 Remote Similarity NPD8306 Approved
0.5948 Remote Similarity NPD8305 Approved
0.5935 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5926 Remote Similarity NPD8394 Approved
0.5895 Remote Similarity NPD3187 Discontinued
0.5887 Remote Similarity NPD8080 Discontinued
0.587 Remote Similarity NPD9033 Approved
0.587 Remote Similarity NPD9030 Approved
0.587 Remote Similarity NPD9032 Approved
0.587 Remote Similarity NPD9031 Approved
0.5868 Remote Similarity NPD6936 Clinical (unspecified phase)
0.5868 Remote Similarity NPD6935 Phase 3
0.5865 Remote Similarity NPD3200 Clinical (unspecified phase)
0.5833 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5825 Remote Similarity NPD361 Discontinued
0.581 Remote Similarity NPD3203 Approved
0.581 Remote Similarity NPD3201 Approved
0.581 Remote Similarity NPD3209 Approved
0.581 Remote Similarity NPD2698 Approved
0.581 Remote Similarity NPD3207 Approved
0.581 Remote Similarity NPD3208 Approved
0.581 Remote Similarity NPD3202 Approved
0.5789 Remote Similarity NPD8276 Approved
0.5789 Remote Similarity NPD8275 Approved
0.5702 Remote Similarity NPD8086 Approved
0.5702 Remote Similarity NPD8085 Approved
0.5702 Remote Similarity NPD8082 Approved
0.5702 Remote Similarity NPD8139 Approved
0.5702 Remote Similarity NPD8084 Approved
0.5702 Remote Similarity NPD8083 Approved
0.5702 Remote Similarity NPD8138 Approved
0.5701 Remote Similarity NPD5794 Approved
0.5701 Remote Similarity NPD5798 Approved
0.5701 Remote Similarity NPD5795 Approved
0.5701 Remote Similarity NPD5796 Clinical (unspecified phase)
0.5701 Remote Similarity NPD5797 Approved
0.5699 Remote Similarity NPD5380 Approved
0.569 Remote Similarity NPD8393 Approved
0.5676 Remote Similarity NPD3191 Approved
0.5676 Remote Similarity NPD3189 Approved
0.5676 Remote Similarity NPD3190 Approved
0.567 Remote Similarity NPD67 Phase 2
0.567 Remote Similarity NPD9034 Approved
0.5664 Remote Similarity NPD4836 Approved
0.5664 Remote Similarity NPD4838 Approved
0.5664 Remote Similarity NPD4835 Approved
0.5664 Remote Similarity NPD4837 Approved
0.5652 Remote Similarity NPD1457 Discontinued
0.5648 Remote Similarity NPD3168 Discontinued
0.5647 Remote Similarity NPD2269 Approved
0.5641 Remote Similarity NPD8307 Discontinued
0.5641 Remote Similarity NPD8140 Approved
0.5639 Remote Similarity NPD8415 Approved
0.5631 Remote Similarity NPD882 Phase 2
0.5631 Remote Similarity NPD883 Phase 2
0.5606 Remote Similarity NPD8449 Approved
0.5603 Remote Similarity NPD8081 Approved
0.56 Remote Similarity NPD3160 Suspended

  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