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
3vpb ADP Glutamate--LysW ligase ArgX 6.3.2

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 1.155
3wnz ADPAlanine--anticapsin ligase / 0.937
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.889
3wo0 ADPAlanine--anticapsin ligase / 0.871
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.836
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.823
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.800
4ffl ADPUncharacterized protein / 0.800
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.796
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.790
2p0a ANPSynapsin-3 / 0.783
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.777
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.777
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.770
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.769
2hgs ADPGlutathione synthetase 6.3.2.3 0.767
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.767
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.764
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.764
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.761
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.761
5c1o ANPD-alanine--D-alanine ligase / 0.760
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.758
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.755
5c1p ADPD-alanine--D-alanine ligase / 0.754
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.752
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.746
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.746
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.744
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.742
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.741
4fu0 ADPD-alanine--D-alanine ligase / 0.741
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.740
3gu5 ANPDeath-associated protein kinase 1 2.7.11.1 0.740
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.740
4r8q ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.740
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.739
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.738
3rv4 ADPBiotin carboxylase 6.3.4.14 0.737
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.735
1px2 ATPSynapsin-1 / 0.735
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.735
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.732
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.730
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.728
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.727
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.727
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.725
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.725
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.723
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.722
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.720
1aux AGSSynapsin-1 / 0.715
3eth ATPN5-carboxyaminoimidazole ribonucleotide synthase / 0.715
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.715
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.715
3wo1 ADPAlanine--anticapsin ligase / 0.714
4oav ACP2-5A-dependent ribonuclease 3.1.26 0.714
5ce3 ADPProtein kinase YopO / 0.714
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.712
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.712
4dee ADPAurora kinase A 2.7.11.1 0.712
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.711
1pk8 ATPSynapsin-1 / 0.709
4xw4 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.709
3g8d ADPBiotin carboxylase 6.3.4.14 0.708
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.705
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.705
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.704
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.703
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.702
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.702
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.702
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.699
1jbp ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.698
4a2b AGSCell division protein FtsA / 0.698
3idc ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.697
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.697
4ffr ATPUncharacterized protein / 0.697
2j9g ANPBiotin carboxylase 6.3.4.14 0.696
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.696
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.695
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.695
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.695
1lp4 ANPCasein kinase II subunit alpha 2.7.11.1 0.694
4s33 ANPMitogen-activated protein kinase 1 2.7.11.24 0.693
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.691
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.689
5jqw ADPN5-carboxyaminoimidazole ribonucleotide synthase / 0.689
3oii SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.686
4eom ATPCyclin-dependent kinase 2 2.7.11.22 0.686
2b0q ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.685
4ol0 GTPGTP-binding nuclear protein Ran / 0.684
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.682
4cng SAHSpoU rRNA methylase / 0.682
4ffm ADPUncharacterized protein / 0.682
4qny ANPMitogen activated protein kinase, putative / 0.682
4zs4 ATPMyosin heavy chain kinase A 2.7.11.7 0.682
3mhy ATPNitrogen regulatory protein P-II 1 / 0.681
1dv2 ATPBiotin carboxylase 6.3.4.14 0.680
3pdt ADPMyosin heavy chain kinase A 2.7.11.7 0.680
4ocp ADPN-acetylhexosamine 1-kinase 2.7.1.162 0.680
1mq4 ADPAurora kinase A 2.7.11.1 0.678
3mia ANPCyclin-dependent kinase 9 2.7.11.22 0.678
2r86 ATP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.677
4o1p ANPRibonuclease L / 0.677
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.676
3eps ATPIsocitrate dehydrogenase kinase/phosphatase / 0.675
4fj5 DTPDNA-directed DNA polymerase / 0.675
1cm8 ANPMitogen-activated protein kinase 12 / 0.674
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.673
4dn5 AGSMitogen-activated protein kinase kinase kinase 14 2.7.11.25 0.672
5dmz ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.672
2hen ADPEphrin type-B receptor 2 2.7.10.1 0.671
3tm0 ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.671
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.671
4utd ACPAurora kinase A 2.7.11.1 0.671
5bpf ADPD-alanine--D-alanine ligase / 0.671
4fak SAMRibosomal RNA large subunit methyltransferase H / 0.670
1m0w ANPGlutathione synthetase 6.3.2.3 0.669
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.669
2zxu DSTtRNA dimethylallyltransferase 2.5.1.75 0.669
4bn1 ADPAurora kinase A 2.7.11.1 0.669
5dn3 ATPAurora kinase A 2.7.11.1 0.669
1svm ATPLarge T antigen 3.6.4 0.668
2z4w 749Geranylgeranyl pyrophosphate synthase / 0.668
3g8c ADPBiotin carboxylase 6.3.4.14 0.668
4ib3 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.668
4ork GDPBifunctional AAC/APH 2.3.1 0.668
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.667
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.666
2j9g ADPBiotin carboxylase 6.3.4.14 0.666
5iqh GNPBifunctional AAC/APH 2.3.1 0.665
1q8y ADPSerine/threonine-protein kinase SKY1 2.7.11.1 0.664
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.664
4n57 ADPAPH(2'')-Id / 0.664
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.663
1qmz ATPCyclin-dependent kinase 2 2.7.11.22 0.663
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.663
3cly ACPFibroblast growth factor receptor 2 / 0.663
2i8c ADPD-alanine--D-alanine ligase / 0.662
2qo7 ANPEphrin type-A receptor 3 2.7.10.1 0.662
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.662
4zol ACPTubulin tyrosine ligase / 0.662
5dt3 ATPAurora kinase A 2.7.11.1 0.662
2emu SAHDiphthine synthase / 0.661
2qmm SAMtRNA (pseudouridine(54)-N(1))-methyltransferase / 0.661
3af1 GDPPantothenate kinase 2.7.1.33 0.660
3vhx GTPADP-ribosylation factor 6 / 0.660
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.660
1ig1 ANPDeath-associated protein kinase 1 2.7.11.1 0.659
2egw SAHRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.659
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.659
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.659
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.658
4jlb ADPAdenylate kinase / 0.658
2cx8 SAHRibosomal RNA small subunit methyltransferase E / 0.657
4aff ATPNitrogen regulatory protein P-II / 0.657
4qm6 GTPMetallophosphoesterase / 0.657
4ysj ADPCalmodulin-like domain protein kinase / 0.657
4zme ADNMyosin heavy chain kinase A 2.7.11.7 0.657
2dv5 SAHDiphthine synthase / 0.656
5e9e ANPMyosin heavy chain kinase A 2.7.11.7 0.655
2e16 SAHDiphthine synthase / 0.654
4jwj SAHtRNA (guanine(9)-N1)-methyltransferase / 0.654
1k5d GNPGTP-binding nuclear protein Ran / 0.653
1kp2 ATPArgininosuccinate synthase 6.3.4.5 0.653
1wdt GTPElongation factor G (EF-G-2) / 0.653
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.653
3sup DCPDNA-directed DNA polymerase / 0.652
2e15 SAHDiphthine synthase / 0.651
2yy8 MTAtRNA (cytidine(56)-2'-O)-methyltransferase / 0.651
2zdg ADPD-alanine--D-alanine ligase / 0.651
3tw6 ADPPyruvate carboxylase / 0.651
3ufx GDPSuccinate--CoA ligase [GDP-forming] subunit beta / 0.651
4ix6 ADPUncharacterized protein / 0.651
2p6d SAHDiphthine synthase / 0.650
3bbd SAHRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.650
4xbo SAHtRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ 2.1.1.200 0.650