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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
3rv4 ADP Biotin carboxylase 6.3.4.14

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3rv4 ADPBiotin carboxylase 6.3.4.14 1.131
2vqd AP2Biotin carboxylase 6.3.4.14 1.018
2j9g ADPBiotin carboxylase 6.3.4.14 1.014
3tw6 ADPPyruvate carboxylase / 0.894
3g8c ADPBiotin carboxylase 6.3.4.14 0.841
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.813
2b9i ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.791
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.785
1z2n ADPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.783
3t9a ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.778
4nzo ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.777
4ffr ATPUncharacterized protein / 0.773
2pui ADPMethylthioribose kinase 2.7.1.100 0.768
4fu0 ADPD-alanine--D-alanine ligase / 0.765
2r7n ADP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.764
2io8 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.763
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.761
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.756
4ffl ADPUncharacterized protein / 0.755
4iaf ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.753
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.752
1px2 ATPSynapsin-1 / 0.745
4iak ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.745
4k33 ACPFibroblast growth factor receptor 3 2.7.10.1 0.745
4oau ADP2-5A-dependent ribonuclease 3.1.26 0.743
4ifc ADPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.742
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.741
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.741
1zth ADPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.740
3g8d ADPBiotin carboxylase 6.3.4.14 0.740
2io9 ADPBifunctional glutathionylspermidine synthetase/amidase / 0.738
2j9g ANPBiotin carboxylase 6.3.4.14 0.738
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.737
3gu6 ADPDeath-associated protein kinase 1 2.7.11.1 0.733
3t9d ANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.728
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.724
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.722
3t99 ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.721
1dv2 ATPBiotin carboxylase 6.3.4.14 0.720
1z2p ACPInositol-tetrakisphosphate 1-kinase 2.7.1.134 0.720
4ffm ADPUncharacterized protein / 0.719
3k5h ATPPhosphoribosyl-aminoimidazole carboxylase / 0.718
1phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.716
2p0a ANPSynapsin-3 / 0.716
3x2u ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.716
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.715
2py3 ACPFibroblast growth factor receptor 2 / 0.715
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.715
4xlv ACPInsulin receptor 2.7.10.1 0.714
4krc AGSCyclin-dependent protein kinase PHO85 2.7.11.22 0.711
1w2c ANPInositol-trisphosphate 3-kinase A 2.7.1.127 0.708
1jkl ANPDeath-associated protein kinase 1 2.7.11.1 0.707
3vpc ADPGlutamate--LysW ligase ArgX 6.3.2 0.707
3x2v ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.707
4o1p ANPRibonuclease L / 0.707
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.707
2zdg ADPD-alanine--D-alanine ligase / 0.705
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.705
2pml ANPUncharacterized protein / 0.704
4mwh ATPCasein kinase II subunit alpha 2.7.11.1 0.700
1jkk ANPDeath-associated protein kinase 1 2.7.11.1 0.699
4x6r ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.699
3f5u ANPDeath-associated protein kinase 1 2.7.11.1 0.698
4ib3 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.698
3c4z ADPRhodopsin kinase / 0.697
3wnz ADPAlanine--anticapsin ligase / 0.696
4ekk ANPRAC-alpha serine/threonine-protein kinase 2.7.11.1 0.696
1j7l ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.694
3cly ACPFibroblast growth factor receptor 2 / 0.694
5e92 ANPTGF-beta receptor type-2 2.7.11.30 0.694
3gu7 ADPDeath-associated protein kinase 1 2.7.11.1 0.693
4iir ANPSerine/threonine-protein kinase PRP4 homolog 2.7.11.1 0.693
3wo0 ADPAlanine--anticapsin ligase / 0.692
4i3z ADPCyclin-dependent kinase 2 2.7.11.22 0.692
1pk8 ATPSynapsin-1 / 0.691
1daw ANPCasein kinase II subunit alpha 2.7.11.1 0.689
3qwp SAMHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.689
4o4d ATPKinase / 0.688
1j1c ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.687
1aux AGSSynapsin-1 / 0.686
1pyx ANPGlycogen synthase kinase-3 beta 2.7.11.26 0.686
3akk ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.686
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.686
2wq7 FADRE11660p / 0.685
4nm5 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.685
2qcs ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.684
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.684
2y9q ANPMitogen-activated protein kinase 1 2.7.11.24 0.683
3att ATPPutative aminoglycoside phosphotransferase 2.7.1 0.683
4crs AGSSerine/threonine-protein kinase N2 2.7.11.13 0.683
3cvu FADRE11660p / 0.682
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.682
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.682
3niz ADPCdc2-like CDK2/CDC28 like protein kinase / 0.682
5awm ANPStress-activated protein kinase JNK 2.7.11.24 0.682
1csn ATPCasein kinase I homolog 1 2.7.11.1 0.681
1zp9 ATPRIO-type serine/threonine-protein kinase Rio1 2.7.11.1 0.681
4pzk SAHPutative tRNA (cytidine(34)-2'-O)-methyltransferase / 0.681
4zgn ATPCell division cycle protein 123 / 0.681
4gyi ADPUncharacterized protein / 0.680
1j7u ANPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.679
3t54 ATPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.678
5cvh ADPCasein kinase II subunit alpha 2.7.11.1 0.678
3a7h ATPSerine/threonine-protein kinase 24 2.7.11.1 0.677
3llt ANPProtein serine/threonine kinase-1 / 0.677
4fi1 ATPCasein kinase II subunit alpha 2.7.11.1 0.677
4wbb ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.677
5dt4 ATPAurora kinase A 2.7.11.1 0.677
2xrw ANPMitogen-activated protein kinase 8 2.7.11.24 0.676
3cvy FADRE11660p / 0.676
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.674
4lfi GNPCasein kinase II subunit alpha 2.7.11.1 0.674
1a9x ADPCarbamoyl-phosphate synthase large chain / 0.672
1m0w ANPGlutathione synthetase 6.3.2.3 0.672
4ej7 ATPAminoglycoside 3'-phosphotransferase AphA1-IAB / 0.672
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.671
4aw1 ATP3-phosphoinositide-dependent protein kinase 1 2.7.11.1 0.671
4cnf MTASpoU rRNA methylase / 0.671
5dr2 ATPAurora kinase A 2.7.11.1 0.671
4cng SAHSpoU rRNA methylase / 0.670
3lmh ADPMyosin heavy chain kinase A 2.7.11.7 0.669
4iaz ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.669
2pz5 ACPFibroblast growth factor receptor 2 / 0.668
2vp2 DGTDeoxynucleoside kinase / 0.668
2if8 ADPInositol polyphosphate multikinase 2.7.1.151 0.667
3c50 ADPRhodopsin kinase / 0.667
4nm7 ADPGlycogen synthase kinase-3 beta 2.7.11.26 0.667
1mqb ANPEphrin type-A receptor 2 2.7.10.1 0.666
2w4j ADPDeath-associated protein kinase 1 2.7.11.1 0.666
3ez6 ADPPlasmid partition protein A / 0.666
2r86 ATP5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 0.665
4qpm ADPMitotic checkpoint serine/threonine-protein kinase BUB1 2.7.11.1 0.665
5iqi GNPBifunctional AAC/APH 2.3.1 0.665
1mq4 ADPAurora kinase A 2.7.11.1 0.664
1zar ADPRIO-type serine/threonine-protein kinase Rio2 2.7.11.1 0.663
4h12 SAHHistone-lysine N-methyltransferase SETD2 2.1.1.43 0.663
5ce3 ADPProtein kinase YopO / 0.663
5dt3 ATPAurora kinase A 2.7.11.1 0.663
2aky AP5Adenylate kinase / 0.662
3dl0 AP5Adenylate kinase / 0.662
4dee ADPAurora kinase A 2.7.11.1 0.662
4dh5 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.662
4iay ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.662
4mv1 ADPBiotin carboxylase 6.3.4.14 0.662
3akl ADPSerine/threonine-protein kinase CtkA 2.7.11.1 0.661
3b6p TMPThree-prime repair exonuclease 1 3.1.11.2 0.661
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.660
4bga ADPPredicted molecular chaperone distantly related to HSP70-fold metalloproteases / 0.660
4iai ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.660
4lrj ANPUncharacterized protein / 0.660
4o4i ACPTubulin tyrosine ligase / 0.660
3aky AP5Adenylate kinase / 0.659
3dzi RGTADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 3.2.2.6 0.659
4ysj ADPCalmodulin-like domain protein kinase / 0.658
4zme ADNMyosin heavy chain kinase A 2.7.11.7 0.658
2io7 ANPBifunctional glutathionylspermidine synthetase/amidase / 0.657
2pun ACPMethylthioribose kinase 2.7.1.100 0.657
4hpt ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.657
4jl8 ADPAdenylate kinase / 0.657
4mv3 ACPBiotin carboxylase 6.3.4.14 0.657
2e5a LAQLipoyltransferase 1, mitochondrial 2.3.1 0.656
4jsy GTPMetallophosphoesterase / 0.656
4oa9 ANPProtein BRASSINOSTEROID INSENSITIVE 1 2.7.10.1 0.656
2p2m PRXAcetyl-coenzyme A synthetase / 0.655
2pzp ACPFibroblast growth factor receptor 2 / 0.655
3dnt ATPSerine/threonine-protein kinase toxin HipA / 0.655
3w8q AGSDual specificity mitogen-activated protein kinase kinase 1 2.7.12.2 0.655
4ii5 ADPCyclin-dependent kinase 2 2.7.11.22 0.655
4r9u ANPVitamin B12 import ATP-binding protein BtuD / 0.654
4riy ADPEpidermal growth factor receptor 2.7.10.1 0.654
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.653
4iad ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.653
4otp ADPSerine/threonine-protein kinase RIO1 2.7.11.1 0.653
3qak UKAAdenosine receptor A2a / 0.653
1o6y ACPSerine/threonine-protein kinase PknB 2.7.11.1 0.652
2phk ATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform 2.7.11.19 0.652
2xs0 ANPMitogen-activated protein kinase 8 2.7.11.24 0.652
4fjj TTPDNA-directed DNA polymerase / 0.652
4y12 AGSSerine/threonine-protein kinase PknG 2.7.11.1 0.652
3vqx BLKPyrrolysine--tRNA ligase / 0.651
5dn3 ATPAurora kinase A 2.7.11.1 0.651
1ol6 ATPAurora kinase A 2.7.11.1 0.650
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.650
3lu1 UD2UDP-N-acetylglucosamine 4-epimerase / 0.650
3lzj CTPDNA-directed DNA polymerase / 0.650
3mia ANPCyclin-dependent kinase 9 2.7.11.22 0.650
3sup DCPDNA-directed DNA polymerase / 0.650
4o4f ATPKinase / 0.650
5eg3 ACPFibroblast growth factor receptor 2 / 0.650