Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Distribution of Interaction pattern similarity measured by Grim
You can zoom onto the graph by using the mouse to make a selection

Binding Modes are compared using Grim.
For more information, please see the following publication: Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65


Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
3mhy ATP Nitrogen regulatory protein P-II 1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3mhy ATPNitrogen regulatory protein P-II 1 / 1.286
2xul ATPNitrogen regulatory protein P-II / 1.124
4aff ATPNitrogen regulatory protein P-II / 0.864
3ta2 ATPNitrogen regulatory protein P-II (GlnB-3) / 0.775
3ta0 ATPNitrogen regulatory protein P-II (GlnB-3) / 0.759
4fvq ATPTyrosine-protein kinase JAK2 / 0.733
4usj ATPNitrogen regulatory protein PII / 0.713
5i4n ATPTyrosine-protein kinase JAK2 / 0.710
4fvr ATPTyrosine-protein kinase JAK2 / 0.700
2bku GTPGTP-binding nuclear protein Ran / 0.698
1t91 GTPRas-related protein Rab-7a / 0.690
4o4l GTPTubulin alpha-1B chain / 0.690
3wo0 ADPAlanine--anticapsin ligase / 0.689
3n0y APCAdenylate cyclase 2 / 0.688
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.687
4tv9 GTPTubulin alpha-1B chain / 0.686
1ih8 APCNH(3)-dependent NAD(+) synthetase 6.3.1.5 0.685
4ihj GTPTubulin alpha-1B chain / 0.685
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.681
3ez3 ZOLFarnesyl pyrophosphate synthase, putative / 0.680
4lfv YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.678
1xs4 DCPdCTP deaminase / 0.677
1gwn GTPRho-related GTP-binding protein RhoE / 0.675
4iij GTPTubulin alpha-1B chain / 0.675
1sxj AGSReplication factor C subunit 1 / 0.672
4zol GTPTubulin alpha-1B chain / 0.672
2gil GTPRas-related protein Rab-6A / 0.671
3w3z GTPGTP-binding nuclear protein Ran / 0.671
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.671
4ol0 GTPGTP-binding nuclear protein Ran / 0.671
2wgh DTPRibonucleoside-diphosphate reductase large subunit 1.17.4.1 0.670
3wnz ADPAlanine--anticapsin ligase / 0.670
3dyh 721Farnesyl pyrophosphate synthase / 0.669
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.669
3qbt GNPRas-related protein Rab-8A / 0.669
4yvz 3ATDNA integrity scanning protein DisA / 0.669
1p52 ADPArginine kinase 2.7.3.3 0.668
4kvg GTPRas-related protein Rap-1A / 0.668
1wdt GTPElongation factor G (EF-G-2) / 0.667
1yv5 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.667
4qm6 GTPMetallophosphoesterase / 0.667
2c5l GTPGTPase HRas / 0.666
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.666
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.666
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.666
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.665
3s87 DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.665
3wyf GTPGTP-binding nuclear protein / 0.665
4ozn ATPAmmonium transporter / 0.665
3k9l GNPGTPase HRas / 0.664
3s8a DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.664
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.663
1rqj RISFarnesyl diphosphate synthase 2.5.1.10 0.663
1xbt TTPThymidine kinase, cytosolic 2.7.1.21 0.663
2cvx DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.663
2qmm SAMtRNA (pseudouridine(54)-N(1))-methyltransferase / 0.663
4khy TTPDNA-directed DNA polymerase / 0.663
4zwg DTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.663
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.662
4h5e YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.662
1zw5 ZOLFarnesyl pyrophosphate synthase 2.5.1.10 0.661
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.661
4cnf MTASpoU rRNA methylase / 0.661
5c03 AGSNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.661
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.659
1m7b GTPRho-related GTP-binding protein RhoE / 0.658
1zbd GTPRas-related protein Rab-3A / 0.658
4tnq TTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.657
1xts GTPGTP-binding protein Rheb / 0.656
2xzw ATPNitrogen regulatory protein P-II / 0.656
3m0e ATPTranscriptional regulator (NtrC family) / 0.656
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.656
4n57 ADPAPH(2'')-Id / 0.656
2rgx AP5Adenylate kinase / 0.655
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.655
4cng SAHSpoU rRNA methylase / 0.655
1xjj DGTVitamin B12-dependent ribonucleotide reductase / 0.654
2j9g ADPBiotin carboxylase 6.3.4.14 0.654
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.654
3ryh GTPTubulin alpha chain / 0.654
3tgp GNPGTPase HRas / 0.654
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.654
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.654
4qnr ATPPsp operon transcriptional activator / 0.654
5di3 GNPADP-ribosylation factor-like protein 3 / 0.654
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.653
1wa5 GTPGTP-binding nuclear protein Ran / 0.653
4dso GSPGTPase KRas / 0.653
4rwn APC2'-5'-oligoadenylate synthase 1 2.7.7.84 0.653
5itz GTPTubulin alpha-1B chain / 0.653
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.652
2xtn GTPGTPase IMAP family member 2 / 0.652
3er9 3ATPoly(A) polymerase catalytic subunit 2.7.7.19 0.652
3nbz GTPGTP-binding nuclear protein Ran / 0.652
1fmw ATPMyosin-2 heavy chain / 0.651
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.651
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.651
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.651
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.651
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.651
4xoi GTPTransforming protein RhoA / 0.651
2cea ADPATP-dependent zinc metalloprotease FtsH / 0.650
2ha8 SAHProbable methyltransferase TARBP1 / 0.650
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.650
3vth APCCarbamoyltransferase / 0.650
4mkf AP5Adenylate kinase / 0.650
4r39 ANPBlue-light-activated histidine kinase 2 2.7.13.3 0.650
4yj2 GTPTubulin alpha-1B chain / 0.650
5dac AGSUncharacterized protein / 0.650
5jqg GTPTubulin alpha-1B chain / 0.650