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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
1gqy ACP UDP-N-acetylmuramate--L-alanine ligase 6.3.2.8

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 1.289
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 1.139
2vos ADPFolylpolyglutamate synthase / 0.949
2vor ACPFolylpolyglutamate synthase / 0.902
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.899
1w7k ADPDihydrofolate synthase/folylpolyglutamate synthase 6.3.2.12 0.847
3pyz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.844
4dsn GCPGTPase KRas / 0.820
3q9l ATPSeptum site-determining protein MinD / 0.814
4xvu ATPATPase GET3 / 0.808
3zl8 ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.798
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.785
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.783
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.778
1esn ANPPantothenate kinase 2.7.1.33 0.777
2c5l GTPGTPase HRas / 0.772
2j5x GSPADP-ribosylation factor 6 / 0.767
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.767
5l3s GNPSignal recognition particle receptor FtsY / 0.761
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.759
1yzq GNPRas-related protein Rab-6A / 0.758
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.758
1ow3 GDPTransforming protein RhoA / 0.757
1rj9 GCPSignal recognition particle receptor FtsY / 0.757
4xoi GTPTransforming protein RhoA / 0.757
3i3s GNPGTPase HRas / 0.755
4jjz ADPFormate--tetrahydrofolate ligase / 0.754
5dif GNPGTP-binding nuclear protein Ran / 0.754
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.753
5l3r GCPCell division protein FtsY homolog, chloroplastic / 0.753
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.752
1wdt GTPElongation factor G (EF-G-2) / 0.752
4cf7 ADPAdenylate kinase / 0.752
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.751
3l8y GNPGTPase HRas / 0.751
4dls GNPGTPase HRas / 0.750
4dlz GNPGTPase HRas / 0.750
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.749
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.748
2jj1 ADPATP synthase subunit alpha, mitochondrial / 0.748
2jj1 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.748
5k5z ANPUncharacterized protein / 0.748
1xtr GNPGTP-binding protein Rheb / 0.745
1t91 GTPRas-related protein Rab-7a / 0.744
1z2a GDPRas-related protein Rab-23 / 0.744
3k8y GNPGTPase HRas / 0.744
4dlv GNPGTPase HRas / 0.744
4nyj GNPGTPase HRas / 0.744
5ftc ADPTPR domain protein / 0.744
1cxz GSPTransforming protein RhoA / 0.743
4dlx GNPGTPase HRas / 0.743
1d5c GDPGTPase (Rab6) / 0.742
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.742
3rs5 GNPGTPase HRas / 0.742
3tkl GTPRas-related protein Rab-1A / 0.742
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.740
1yu9 GNPRas-related protein Rab-4A / 0.740
2bme GNPRas-related protein Rab-4A / 0.739
4dlw GNPGTPase HRas / 0.739
4q03 GDPGTPase KRas / 0.739
1bmf ADPATP synthase subunit alpha, mitochondrial / 0.737
1bmf ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.737
2j7p GNPSignal recognition particle protein / 0.737
2j7p GNPSignal recognition particle receptor FtsY / 0.737
2rgc GNPGTPase HRas / 0.737
3rs4 GNPGTPase HRas / 0.737
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.737
1n6l GTPRas-related protein Rab-5A / 0.736
3w3z GTPGTP-binding nuclear protein Ran / 0.736
3oiu GNPGTPase HRas / 0.735
2fna ADPUncharacterized protein / 0.734
4hdq GNPRas-related protein Rap-1b / 0.734
4js0 GNPCell division control protein 42 homolog / 0.734
3v4f GNPGTPase HRas / 0.733
5b2z GNPGTPase HRas / 0.733
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.732
5jlj GNPGTP-binding nuclear protein Ran / 0.731
1ky2 GNPGTP-binding protein YPT7 / 0.730
3pit GNPRas-related protein M-Ras / 0.730
4ap0 ADPKinesin-like protein KIF11 / 0.730
2ce2 GDPGTPase HRas / 0.729
3lbi GNPGTPase HRas / 0.729
4x8o AP5Adenylate kinase / 0.729
4ylg GDPADP-ribosylation factor 1, putative / 0.729
4g0n GNPGTPase HRas / 0.728
4y0v GDPADP-ribosylation factor 1, putative / 0.728
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.727
2fju GSPRas-related C3 botulinum toxin substrate 1 / 0.727
4kvg GTPRas-related protein Rap-1A / 0.727
4o2l GTPGTP-binding protein Rheb / 0.727
4rkf GNPRas-related protein Rab-3 / 0.727
2xae ADPKinesin-like protein KIF11 / 0.726
4nh0 ATPESX secretion system protein EccC / 0.726
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.725
3rs7 GNPGTPase HRas / 0.725
4uj3 GNPRas-related protein Rab-11A / 0.723
1w5t ANPORC1-type DNA replication protein 2 / 0.722
1z2c GNPRho-related GTP-binding protein RhoC / 0.722
3rsl GNPGTPase HRas / 0.721
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.720
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.719
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.719
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.719
3ea5 GDPGTP-binding nuclear protein Ran / 0.719
3rs0 GNPGTPase HRas / 0.719
4ql3 GDPGTPase KRas / 0.719
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.717
2rge GNPGTPase HRas / 0.717
3ref GDPRho family GTPase / 0.717
4ihq ADPConserved Archaeal protein / 0.717
4cid ANPEH domain-containing protein 2 / 0.716
4jld ADPAdenylate kinase / 0.716
4luc GDPGTPase KRas / 0.716
4r9u ANPVitamin B12 import ATP-binding protein BtuD / 0.716
1gwn GTPRho-related GTP-binding protein RhoE / 0.714
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.714
3oiv GNPGTPase HRas / 0.714
5di3 GNPADP-ribosylation factor-like protein 3 / 0.714
4dzz ADPPlasmid partitioning protein ParF / 0.713
4l8g GDPGTPase KRas / 0.713
2gcp GSPRho-related GTP-binding protein RhoC / 0.712
3r9i ADPSeptum site-determining protein MinD / 0.712
1ank ANPAdenylate kinase / 0.711
1ayl ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.710
1z0d GDPRas-related protein Rab-5C / 0.710
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.710
4dso GSPGTPase KRas / 0.710
3tgp GNPGTPase HRas / 0.709
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.708
2x7e ADPKinesin-like protein KIF11 / 0.708
3x1z GNPRas-related protein Rap-1b / 0.708
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.707
1x1r GDPRas-related protein M-Ras / 0.707
3oee ANPATP synthase subunit alpha, mitochondrial / 0.707
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.707
1g17 GNPRas-related protein SEC4 / 0.706
1kmq GNPTransforming protein RhoA / 0.706
3oiw GNPGTPase HRas / 0.706
3x1w GDPRas-related protein Rap-1b / 0.706
4epw GDPGTPase KRas / 0.706
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.706
5dha GNPGTP-binding nuclear protein Ran / 0.706
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.705
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.705
4v02 ATPSite-determining protein / 0.705
1z0a GDPRas-related protein Rab-2A / 0.704
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.704
3zfd ANPChromosome-associated kinesin KIF4 / 0.704
2q3f GNPRas-related GTP-binding protein D / 0.703
2dpx GDPGTP-binding protein RAD / 0.702
1khe GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.701
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.699
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.699
2rgg GNPGTPase HRas / 0.699
3zia ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.698
3k9l GNPGTPase HRas / 0.697
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.696
3k1j ADPATP-dependent protease Lon / 0.696
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.696
1uad GNPRas-related protein Ral-A / 0.695
1z0f GDPRas-related protein Rab-14 / 0.695
2bku GTPGTP-binding nuclear protein Ran / 0.695
2fe4 GDPRas-related protein Rab-6B / 0.694
4hdo GNPRas-related protein Rap-1b / 0.694
5fl3 ADPPili retraction protein PilT / 0.694
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.693
2uyi ADPKinesin-like protein KIF11 / 0.693
3c41 ANPAmino acid ABC transporter / 0.693
2x2r ADPKinesin-like protein KIF11 / 0.692
3lbn GNPGTPase HRas / 0.692
1fmw ATPMyosin-2 heavy chain / 0.690
2bc9 GNPGuanylate-binding protein 1 / 0.690
2y65 ADPKinesin heavy chain / 0.690
3tso GNPRas-related protein Rab-25 / 0.690
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.689
1m7b GTPRho-related GTP-binding protein RhoE / 0.688
4xsg GSPTransforming protein RhoA / 0.688
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.687
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.687
2fgk ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.687
2pg2 ADPKinesin-like protein KIF11 / 0.687
3cob ADPKinesin heavy chain-like protein / 0.687
3e5h GNPRas-related protein Rab-28 / 0.687
4a1z ADPKinesin-like protein KIF11 / 0.687
1e1q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.684
3cph GDPRas-related protein SEC4 / 0.684
3l1c ADPProtein claret segregational / 0.684
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.684
4idp GNPAtlastin-1 3.6.5 0.684
1wbb ADPDNA mismatch repair protein MutS / 0.683
3rab GNPRas-related protein Rab-3A / 0.683
4dsu GDPGTPase KRas / 0.683
4epx GDPGTPase KRas / 0.683
4idn GNPAtlastin-1 3.6.5 0.683
4l9s GDPGTPase HRas / 0.683
1mmg AGSMyosin-2 heavy chain / 0.682
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.682
4bec ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.682
3tjz GNPADP-ribosylation factor 1 / 0.681
3vhx GTPADP-ribosylation factor 6 / 0.681
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.681
4tq9 GDPGTPase KRas / 0.681
4l9w GNPGTPase HRas / 0.680
1oix GDPRas-related protein Rab-11A / 0.679
1vg8 GNPRas-related protein Rab-7a / 0.679
2gil GTPRas-related protein Rab-6A / 0.679
3thy ADPDNA mismatch repair protein Msh2 / 0.679
4qm6 GTPMetallophosphoesterase / 0.679
1k5d GNPGTP-binding nuclear protein Ran / 0.678
4a28 ADPKinesin-like protein KIF11 / 0.678
1mma ADPMyosin-2 heavy chain / 0.677
1tu3 GNPRas-related protein Rab-5A / 0.676
2zrj AGSProtein RecA / 0.676
4jl5 ADPAdenylate kinase / 0.676
3mjh GTPRas-related protein Rab-5A / 0.675
1b7t ADPMyosin heavy chain, striated muscle / 0.674
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.674
1okk GCPSignal recognition particle protein / 0.674
1okk GCPSignal recognition particle receptor FtsY / 0.674
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.674
3bos CDPRegulatory inactivation of DnaA Hda protein / 0.674
4pjk ADPMyosin-2 heavy chain / 0.674
4pk4 ADPUnconventional myosin-VI / 0.674
3ftq GNPSeptin-2 / 0.673
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.673
5c3z ACPRibokinase / 0.673
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.672
2ql6 ADPNicotinamide riboside kinase 1 / 0.672
1sdm ADPKinesin heavy chain-like protein / 0.671
4obe GDPGTPase KRas / 0.671
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.671
1nly AGSCag alpha / 0.670
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.670
4xvr GNPGTPase HRas / 0.670
1svm ATPLarge T antigen 3.6.4 0.669
3qbt GNPRas-related protein Rab-8A / 0.669
4ys0 ADPProtein translocase subunit SecA / 0.669
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.668
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.667
4dvg GSPRho family GTPase / 0.667
3b05 IPEIsopentenyl-diphosphate delta-isomerase / 0.666
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.666
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.665
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.665
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.665
3k3b ADPKinesin-like protein KIF11 / 0.665
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.664
2v7q ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.664
1ake AP5Adenylate kinase / 0.663
1jx2 ADPMyosin-2 heavy chain / 0.663
1zc4 GNPRas-related protein Ral-A / 0.663
4ohv ANPProtein clpf-1 / 0.663
5c46 GSPRas-related protein Rab-11A / 0.663
3hqd ANPKinesin-like protein KIF11 / 0.662
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.662
1s1c GNPTransforming protein RhoA / 0.661
2fg5 GNPRas-related protein Rab-31 / 0.661
2jlr ANPGenome polyprotein 3.4.21.91 0.661
3tlx ADPAdenylate kinase 2 / 0.661
4z54 GDPNeuronal-specific septin-3 / 0.661
1zc3 GNPRas-related protein Ral-A / 0.660
2cls GTPRho-related GTP-binding protein Rho6 / 0.660
3fkq ATPNtrC-like two-domain protein / 0.660
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.659
3law GNPRas-related protein Rab-7a / 0.659
3ums GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.659
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.658
3kud GDPGTPase HRas / 0.658
3oes GNPGTPase RhebL1 / 0.658
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.658
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.658
5c40 ACPRibokinase / 0.658
1yrs ADPKinesin-like protein KIF11 / 0.657
2eck ADPAdenylate kinase / 0.657
2rgx AP5Adenylate kinase / 0.656
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.656
3myk ANPMyosin-2 heavy chain / 0.656
4jl6 ADPAdenylate kinase / 0.656
4uj5 GNPRas-related protein Rab-11A / 0.656
3bc1 GNPRas-related protein Rab-27A / 0.655
3l9h ADPKinesin-like protein KIF11 / 0.655
4hut ATPCob(I)yrinic acid a,c-diamide adenosyltransferase 2.5.1.17 0.655
1lfd GNPGTPase HRas / 0.654
2ex1 C5PAlpha-2,3/2,6-sialyltransferase/sialidase / 0.654
2zfi ADPKinesin-like protein KIF1A / 0.654
1sq5 ADPPantothenate kinase 2.7.1.33 0.653
1w5s ADPORC1-type DNA replication protein 2 / 0.653
4b7b ADPKinesin-like protein KIF11 / 0.653
1fp6 ADPNitrogenase iron protein 1 1.18.6.1 0.652
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.652
2zpa ADPtRNA(Met) cytidine acetyltransferase TmcA / 0.652
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.652
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.651
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.651
4ldj GDPGTPase KRas / 0.650
4xvq GNPGTPase HRas / 0.650