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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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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
3g8d ADP Biotin carboxylase 6.3.4.14

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3g8d ADPBiotin carboxylase 6.3.4.14 0.973
2j9g ANPBiotin carboxylase 6.3.4.14 0.772
3tw6 ADPPyruvate carboxylase / 0.757
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.754
2vqd AP2Biotin carboxylase 6.3.4.14 0.743
3rv4 ADPBiotin carboxylase 6.3.4.14 0.740
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.739
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.739
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.738
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.738
4fu0 ADPD-alanine--D-alanine ligase / 0.736
2b9f ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.734
2vr1 ATFBiotin carboxylase 6.3.4.14 0.729
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.728
3eps ATPIsocitrate dehydrogenase kinase/phosphatase / 0.726
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.725
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.724
3g8c ADPBiotin carboxylase 6.3.4.14 0.722
4gyi ADPUncharacterized protein / 0.720
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.717
4ffm ADPUncharacterized protein / 0.717
3att ATPPutative aminoglycoside phosphotransferase 2.7.1 0.715
4mv3 ACPBiotin carboxylase 6.3.4.14 0.715
1px2 ATPSynapsin-1 / 0.714
3wnz ADPAlanine--anticapsin ligase / 0.714
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.714
2if8 ADPInositol polyphosphate multikinase 2.7.1.151 0.708
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.708
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.708
5c1p ADPD-alanine--D-alanine ligase / 0.706
4ffl ADPUncharacterized protein / 0.705
5e9e ANPMyosin heavy chain kinase A 2.7.11.7 0.701
3r5f ATPD-alanine--D-alanine ligase / 0.700
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.698
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.697
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.697
4gt3 ATPMitogen-activated protein kinase 1 2.7.11.24 0.694
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.694
2i8c ADPD-alanine--D-alanine ligase / 0.692
2pyw ADPMethylthioribose kinase 2.7.1.100 0.692
1pk8 ATPSynapsin-1 / 0.691
4fl1 ANPTyrosine-protein kinase SYK 2.7.10.2 0.691
3lla ACPMyosin heavy chain kinase A 2.7.11.7 0.690
2zdg ADPD-alanine--D-alanine ligase / 0.689
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.686
4ffr ATPUncharacterized protein / 0.686
1mqb ANPEphrin type-A receptor 2 2.7.10.1 0.684
1zp9 ATPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.684
4iwx ADPRibosomal protein S6--L-glutamate ligase / 0.684
4zme ADNMyosin heavy chain kinase A 2.7.11.7 0.684
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.683
2pup ADPMethylthioribose kinase 2.7.1.100 0.681
2r86 ATP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.677
4iwy ADPRibosomal protein S6--L-glutamate ligase / 0.676
3pdt ADPMyosin heavy chain kinase A 2.7.11.7 0.675
4zs4 ATPMyosin heavy chain kinase A 2.7.11.7 0.675
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.674
2pui ADPMethylthioribose kinase 2.7.1.100 0.673
3wo1 ADPAlanine--anticapsin ligase / 0.670
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.670
4f9a ADPCell division cycle 7-related protein kinase 2.7.11.1 0.669
4iay ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.669
4o4i ACPTubulin tyrosine ligase / 0.669
1mp8 ADPFocal adhesion kinase 1 2.7.10.2 0.668
3o7l ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.668
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.668
5jqw ADPN5-carboxyaminoimidazole ribonucleotide synthase / 0.668
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.667
3akl ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.665
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.665
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.665
1t36 ADPCarbamoyl-phosphate synthase large chain / 0.664
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.664
4o1p ANPRibonuclease L / 0.664
2eb3 ANPEpidermal growth factor receptor 2.7.10.1 0.663
3wo0 ADPAlanine--anticapsin ligase / 0.663
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.662
1aux AGSSynapsin-1 / 0.661
2hgs ADPGlutathione synthetase 6.3.2.3 0.661
4gvj ADPNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.661
4o4d ATPKinase / 0.661
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.660
4cng SAHSpoU rRNA methylase / 0.660
1tqm ANPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.659
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.658
4x6r ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.658
4dt8 ADNAPH(2'')-Id / 0.657
5cns DATRibonucleoside-diphosphate reductase 1 subunit alpha 1.17.4.1 0.657
4riy ADPEpidermal growth factor receptor 2.7.10.1 0.655
1zao ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.654
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.654
3mia ANPCyclin-dependent kinase 9 2.7.11.22 0.654
2hen ADPEphrin type-B receptor 2 2.7.10.1 0.652
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.651
4s34 ANPMitogen-activated protein kinase 1 2.7.11.24 0.651
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.650
1tqp ATPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.650
2pz5 ACPFibroblast growth factor receptor 2 / 0.650
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.650
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.650
5dr2 ATPAurora kinase A 2.7.11.1 0.650