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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
4mkg AP5 Adenylate kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4mkg AP5Adenylate kinase / 1.949
3dkv AP5Adenylate kinase / 1.737
2eu8 AP5Adenylate kinase / 1.725
2qaj AP5Adenylate kinase / 1.689
4mkf AP5Adenylate kinase / 1.662
2oo7 AP5Adenylate kinase / 1.649
4w5j AP5Adenylate kinase / 1.587
3dl0 AP5Adenylate kinase / 1.533
2osb AP5Adenylate kinase / 1.508
4nu0 AP5Adenylate kinase / 1.482
2aky AP5Adenylate kinase / 1.444
3aky AP5Adenylate kinase / 1.294
4qbf AP5Adenylate kinase / 1.165
1p3j AP5Adenylate kinase / 1.141
4qbg AP5Adenylate kinase / 1.133
4mkh AP5Adenylate kinase / 1.087
1s3g AP5Adenylate kinase / 1.063
1zio AP5Adenylate kinase / 1.062
4tyq AP5Adenylate kinase / 1.062
2rgx AP5Adenylate kinase / 1.054
4qbi AP5Adenylate kinase / 1.037
4typ AP5Adenylate kinase / 0.922
4qbh AP5Adenylate kinase / 0.904
4qm6 GTPMetallophosphoesterase / 0.882
4x8o AP5Adenylate kinase / 0.864
4jlp ADPAdenylate kinase / 0.847
4jlo ADPAdenylate kinase / 0.845
4jl5 ADPAdenylate kinase / 0.843
4jld ADPAdenylate kinase / 0.829
4jl6 ADPAdenylate kinase / 0.815
4jlb ADPAdenylate kinase / 0.789
4jky ADPAdenylate kinase / 0.785
4x8l AP5Adenylate kinase / 0.785
1svm ATPLarge T antigen 3.6.4 0.772
1e4v AP5Adenylate kinase / 0.767
4ike ADPAdenylate kinase / 0.764
4jla ADPAdenylate kinase / 0.755
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.752
2ffq GSPRas-related protein Rab-6B / 0.751
1ake AP5Adenylate kinase / 0.748
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.738
3wyf GTPGTP-binding nuclear protein / 0.738
1a2b GSPTransforming protein RhoA / 0.736
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.732
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.728
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.722
3hpr AP5Adenylate kinase / 0.720
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.720
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.719
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.718
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.718
4dvg GSPRho family GTPase / 0.718
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.718
1fmw ATPMyosin-2 heavy chain / 0.717
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.716
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.713
4jl8 ADPAdenylate kinase / 0.713
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.710
4dxa GSPRas-related protein Rap-1b / 0.709
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.708
3tjz GNPADP-ribosylation factor 1 / 0.706
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.702
1gwn GTPRho-related GTP-binding protein RhoE / 0.701
1m7b GTPRho-related GTP-binding protein RhoE / 0.701
4ol0 GTPGTP-binding nuclear protein Ran / 0.701
2c5l GTPGTPase HRas / 0.700
2gcp GSPRho-related GTP-binding protein RhoC / 0.697
3tlx ADPAdenylate kinase 2 / 0.696
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.694
5dac AGSUncharacterized protein / 0.692
1dvr ATFAdenylate kinase / 0.690
2eck ADPAdenylate kinase / 0.689
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.688
1t91 GTPRas-related protein Rab-7a / 0.687
1sq5 ADPPantothenate kinase 2.7.1.33 0.686
1svw GTPProbable GTP-binding protein EngB / 0.686
3hu3 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.686
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.685
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.682
1b7t ADPMyosin heavy chain, striated muscle / 0.679
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.679
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.679
3w3z GTPGTP-binding nuclear protein Ran / 0.679
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.678
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.677
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.677
4q03 GDPGTPase KRas / 0.677
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.676
3hpq AP5Adenylate kinase / 0.676
1zbd GTPRas-related protein Rab-3A / 0.675
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.675
5d3q GDPDynamin-1 3.6.5.5 0.673
3orl AGSSerine/threonine protein kinase / 0.672
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.669
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.669
2xtn GTPGTPase IMAP family member 2 / 0.669
2zet GTPRas-related protein Rab-27B / 0.669
4fvr ATPTyrosine-protein kinase JAK2 / 0.669
4pl0 ANPMicrocin-J25 export ATP-binding/permease protein McjD / 0.669
5i4n ATPTyrosine-protein kinase JAK2 / 0.669
1ank ANPAdenylate kinase / 0.668
3tkl GTPRas-related protein Rab-1A / 0.668
4qxa GTPRas-related protein Rab-9A / 0.668
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.667
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.667
4kvg GTPRas-related protein Rap-1A / 0.667
1sxj AGSReplication factor C subunit 1 / 0.666
3x2w ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.665
4c5c ATPD-alanine--D-alanine ligase B 6.3.2.4 0.665
2gil GTPRas-related protein Rab-6A / 0.664
3pcr GTPADP-ribosylation factor 6 / 0.664
3ryh GTPTubulin alpha chain / 0.664
4brg GNPEctonucleoside triphosphate diphosphohydrolase I / 0.664
4xoi GTPTransforming protein RhoA / 0.664
2bbw GP5Adenylate kinase 4, mitochondrial / 0.662
3bc1 GNPRas-related protein Rab-27A / 0.662
1wa5 GTPGTP-binding nuclear protein Ran / 0.660
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.659
3vtk ADPThymidine kinase / 0.659
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.659
5la6 GTPTubulin alpha-1B chain / 0.659
3vth APCCarbamoyltransferase / 0.657
1o1s 1NHProtein farnesyltransferase subunit beta 2.5.1.58 0.656
5c46 GSPRas-related protein Rab-11A / 0.656
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.655
4s1b 2BALmo1466 protein / 0.655
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.654
3eg5 GNPCell division control protein 42 homolog / 0.654
3tqc ADPPantothenate kinase / 0.654
3c14 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.652
3kz1 GSPTransforming protein RhoA / 0.652
1k5d GNPGTP-binding nuclear protein Ran / 0.651
1o6k ANPRAC-beta serine/threonine-protein kinase 2.7.11.1 0.651
2jib ADPOxalyl-CoA decarboxylase 4.1.1.8 0.651
2z4z SC0Geranylgeranyl pyrophosphate synthase / 0.651
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.650
4xsg GSPTransforming protein RhoA / 0.650