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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
2oo7 AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2oo7 AP5Adenylate kinase / 1.795
2qaj AP5Adenylate kinase / 1.682
2eu8 AP5Adenylate kinase / 1.650
4mkg AP5Adenylate kinase / 1.649
3dl0 AP5Adenylate kinase / 1.594
3dkv AP5Adenylate kinase / 1.529
2osb AP5Adenylate kinase / 1.486
4w5j AP5Adenylate kinase / 1.464
4nu0 AP5Adenylate kinase / 1.454
4mkf AP5Adenylate kinase / 1.363
1p3j AP5Adenylate kinase / 1.332
2aky AP5Adenylate kinase / 1.304
3aky AP5Adenylate kinase / 1.146
1s3g AP5Adenylate kinase / 1.139
1zio AP5Adenylate kinase / 1.139
4qbh AP5Adenylate kinase / 1.081
4qbg AP5Adenylate kinase / 1.039
2rgx AP5Adenylate kinase / 1.000
4tyq AP5Adenylate kinase / 0.985
4qbf AP5Adenylate kinase / 0.972
4mkh AP5Adenylate kinase / 0.965
4typ AP5Adenylate kinase / 0.935
4qbi AP5Adenylate kinase / 0.901
4x8l AP5Adenylate kinase / 0.869
4jlo ADPAdenylate kinase / 0.844
4jl6 ADPAdenylate kinase / 0.843
1e4v AP5Adenylate kinase / 0.834
4qm6 GTPMetallophosphoesterase / 0.833
4jl5 ADPAdenylate kinase / 0.825
4jky ADPAdenylate kinase / 0.812
4jl8 ADPAdenylate kinase / 0.749
4jsy GTPMetallophosphoesterase / 0.749
4x8o AP5Adenylate kinase / 0.748
1svm ATPLarge T antigen 3.6.4 0.745
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.745
4jlb ADPAdenylate kinase / 0.741
4jla ADPAdenylate kinase / 0.731
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.726
4ohx ADPProtein clpf-1 / 0.726
2eck ADPAdenylate kinase / 0.724
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.721
2ffq GSPRas-related protein Rab-6B / 0.718
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.716
4qnr ATPPsp operon transcriptional activator / 0.712
3law GNPRas-related protein Rab-7a / 0.707
1ank ANPAdenylate kinase / 0.706
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 0.706
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.704
1ake AP5Adenylate kinase / 0.701
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.699
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.693
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.693
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.693
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.693
3tqc ADPPantothenate kinase / 0.690
1e4y AP5Adenylate kinase / 0.689
2xtn GTPGTPase IMAP family member 2 / 0.689
3hpr AP5Adenylate kinase / 0.689
4dvg GSPRho family GTPase / 0.688
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.686
2v92 ATP5'-AMP-activated protein kinase subunit gamma-1 / 0.686
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.683
1sxj AGSReplication factor C subunit 1 / 0.680
1svw GTPProbable GTP-binding protein EngB / 0.679
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.679
3m0e ATPTranscriptional regulator (NtrC family) / 0.679
3orl AGSSerine/threonine protein kinase / 0.679
2iut AGSDNA translocase FtsK / 0.677
2gcp GSPRho-related GTP-binding protein RhoC / 0.674
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.672
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.672
5d3q GDPDynamin-1 3.6.5.5 0.672
3oee ANPATP synthase subunit alpha, mitochondrial / 0.671
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.671
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.670
1sdm ADPKinesin heavy chain-like protein / 0.670
4gzm GSPRas-related C3 botulinum toxin substrate 1 / 0.670
5dac AGSUncharacterized protein / 0.669
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.668
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.668
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.668
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.668
2c96 ATPPsp operon transcriptional activator / 0.667
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.664
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.663
3a5m ATPMajor actin / 0.662
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.662
3idb ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.659
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.658
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.658
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.656
1sq5 ADPPantothenate kinase 2.7.1.33 0.655
3ncr ADPNitrogen regulatory protein P-II (GlnB-2) / 0.654
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.653
2bbw GP5Adenylate kinase 4, mitochondrial / 0.652
4qxa GTPRas-related protein Rab-9A / 0.652
1m7b GTPRho-related GTP-binding protein RhoE / 0.651
1w7i ADPUnconventional myosin-Va / 0.651
2cvx DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.651
2jib TPPOxalyl-CoA decarboxylase 4.1.1.8 0.651
2pc9 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.651
3ahe THDProbable phosphoketolase / 0.651
4bur FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.651
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.651
4iac ACPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.651
1xjj DGTVitamin B12-dependent ribonucleotide reductase / 0.650
3tkl GTPRas-related protein Rab-1A / 0.650
3zlm ANPAdenosine monophosphate-protein transferase NmFic 2.7.7.n1 0.650
4cf7 ADPAdenylate kinase / 0.650