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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
4cvm ANP UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4cvm ANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 1.086
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.881
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.808
2vos ADPFolylpolyglutamate synthase / 0.773
2vor ACPFolylpolyglutamate synthase / 0.771
1z2c GNPRho-related GTP-binding protein RhoC / 0.766
3pit GNPRas-related protein M-Ras / 0.760
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.758
3tgp GNPGTPase HRas / 0.758
3x1z GNPRas-related protein Rap-1b / 0.755
1uad GNPRas-related protein Ral-A / 0.752
3ddc GNPGTPase HRas / 0.751
3zfd ANPChromosome-associated kinesin KIF4 / 0.751
4xvq GNPGTPase HRas / 0.751
4xvu ATPATPase GET3 / 0.750
1yu9 GNPRas-related protein Rab-4A / 0.746
2fgj ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.742
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.741
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.739
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.737
4hdq GNPRas-related protein Rap-1b / 0.734
1ibr GNPGTP-binding nuclear protein Ran / 0.733
1s1c GNPTransforming protein RhoA / 0.733
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.732
1esn ANPPantothenate kinase 2.7.1.33 0.731
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.731
4a51 ADPKinesin-like protein KIF11 / 0.730
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.726
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.724
4o2l GTPGTP-binding protein Rheb / 0.722
5k5z ANPUncharacterized protein / 0.721
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.720
4nyi GNPGTPase HRas / 0.720
1lfd GNPGTPase HRas / 0.719
4jjz ADPFormate--tetrahydrofolate ligase / 0.719
4ymu ATPABC-type polar amino acid transport system, ATPase component / 0.719
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.716
4dsn GCPGTPase KRas / 0.716
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA2 3.6.3 0.715
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA1 / 0.715
2fah GDPPhosphoenolpyruvate carboxykinase [GTP], mitochondrial 4.1.1.32 0.713
3vhx GTPADP-ribosylation factor 6 / 0.713
1okk GCPSignal recognition particle protein / 0.712
1okk GCPSignal recognition particle receptor FtsY / 0.712
4yer ADPAntibiotic ABC transporter, ATP-binding protein, putative / 0.711
1xnj ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 2.7.1.25 0.709
3tlx ADPAdenylate kinase 2 / 0.709
4jl5 ADPAdenylate kinase / 0.709
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.708
4idp GNPAtlastin-1 3.6.5 0.708
4jl6 ADPAdenylate kinase / 0.708
3oee ANPATP synthase subunit alpha, mitochondrial / 0.707
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.707
4ike ADPAdenylate kinase / 0.707
4jld ADPAdenylate kinase / 0.706
2eck ADPAdenylate kinase / 0.705
2ql6 ADPNicotinamide riboside kinase 1 / 0.705
4o2r GDPGTP-binding protein Rheb / 0.704
3b05 IPEIsopentenyl-diphosphate delta-isomerase / 0.703
1in5 ADPHolliday junction ATP-dependent DNA helicase RuvB / 0.702
4wa7 GDPGTPase KRas / 0.702
1njf AGSDNA polymerase III subunit tau 2.7.7.7 0.701
1r0z ATPCystic fibrosis transmembrane conductance regulator / 0.701
3d8b ADPFidgetin-like protein 1 3.6.4 0.701
1w7k ADPDihydrofolate synthase/folylpolyglutamate synthase 6.3.2.12 0.700
1ank ANPAdenylate kinase / 0.699
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.695
3qcz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.695
2gks ADPProbable bifunctional SAT/APS kinase 2.7.1.25 0.694
3rab GNPRas-related protein Rab-3A / 0.694
4goj GNPADP-ribosylation factor-like protein 3 / 0.694
4ko8 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.694
2jlr ANPGenome polyprotein 3.4.21.91 0.693
4jlo ADPAdenylate kinase / 0.692
1w5t ANPORC1-type DNA replication protein 2 / 0.691
2hld ANPATP synthase subunit alpha, mitochondrial / 0.691
2hld ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.691
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.691
3tif ADPUncharacterized ABC transporter ATP-binding protein MJ0796 / 0.691
3tqc ADPPantothenate kinase / 0.691
5ckw ANPUncharacterized protein / 0.691
4cf7 ADPAdenylate kinase / 0.690
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.688
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.688
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.688
1g16 GDPRas-related protein SEC4 / 0.687
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.687
1k6m AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 2.7.1.105 0.687
1g6o ADPCag alpha / 0.686
1yra GDPGPN-loop GTPase PAB0955 / 0.686
2xae ADPKinesin-like protein KIF11 / 0.685
3qpv ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.685
5ftc ADPTPR domain protein / 0.685
1p9w ANPType II secretion system protein E / 0.684
2rge GNPGTPase HRas / 0.684
2rgg GNPGTPase HRas / 0.684
1m7b GTPRho-related GTP-binding protein RhoE / 0.683
3l1c ADPProtein claret segregational / 0.683
3lbn GNPGTPase HRas / 0.683
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.682
4ma4 ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.682
1e79 ADPATP synthase subunit alpha, mitochondrial / 0.680
1e79 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.680
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.680
1njf ADPDNA polymerase III subunit tau 2.7.7.7 0.679
1svm ATPLarge T antigen 3.6.4 0.679
4iok ADPFormate--tetrahydrofolate ligase / 0.679
4xsg GSPTransforming protein RhoA / 0.679
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.677
3l9h ADPKinesin-like protein KIF11 / 0.677
1xmv ADPProtein RecA / 0.676
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.676
2zrj AGSProtein RecA / 0.676
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.675
1sq5 ADPPantothenate kinase 2.7.1.33 0.675
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.675
3k1j ADPATP-dependent protease Lon / 0.675
4dvg GSPRho family GTPase / 0.675
4b7b ADPKinesin-like protein KIF11 / 0.673
4dlt GNPGTPase HRas / 0.672
2axn ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 / 0.671
3q9l ATPSeptum site-determining protein MinD / 0.670
4d81 ADPAAA ATPase, central domain protein / 0.670
1rj9 GCPSignal recognition particle receptor FtsY / 0.669
2qen ADPWalker-Type ATPase / 0.669
4r9u ANPVitamin B12 import ATP-binding protein BtuD / 0.669
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.668
1z0d GDPRas-related protein Rab-5C / 0.668
1zbd GTPRas-related protein Rab-3A / 0.668
2ax4 ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.7.1.25 0.667
4hi0 GDPUrease accessory protein UreG / 0.667
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.667
5jlj GNPGTP-binding nuclear protein Ran / 0.667
4xoi GTPTransforming protein RhoA / 0.666
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.664
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.664
2o8b ADPDNA mismatch repair protein Msh2 / 0.664
3ftq GNPSeptin-2 / 0.664
3hu1 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.664
1rrg GDPADP-ribosylation factor 1 / 0.663
1yrs ADPKinesin-like protein KIF11 / 0.663
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.663
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.663
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.663
3ieu GDPGTPase Era / 0.663
1e1q ANPATP synthase subunit alpha, mitochondrial / 0.662
1e1q ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.662
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.662
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.662
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.662
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.662
2fl2 ADPKinesin-like protein KIF11 / 0.661
5c46 GSPRas-related protein Rab-11A / 0.661
1z6t ADPApoptotic protease-activating factor 1 / 0.660
2zts ADPUncharacterized protein / 0.660
1tu3 GNPRas-related protein Rab-5A / 0.659
2q3f GNPRas-related GTP-binding protein D / 0.659
3a58 GNPGTP-binding protein RHO1 / 0.659
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.659
3hqd ANPKinesin-like protein KIF11 / 0.659
4zca ADPKinesin-like protein KIF11 / 0.659
3cph GDPRas-related protein SEC4 / 0.658
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.658
3zlm ANPAdenosine monophosphate-protein transferase NmFic 2.7.7.n1 0.658
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.657
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.657
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.656
4ihq ADPConserved Archaeal protein / 0.656
5bn3 ADPV-type ATP synthase alpha chain / 0.656
5bn3 ADPNEQ263 / 0.656
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.655
1vg8 GNPRas-related protein Rab-7a / 0.654
1w5t ADPORC1-type DNA replication protein 2 / 0.654
2gm1 ADPKinesin-like protein KIF11 / 0.654
2oap ANPType II secretion system protein (GspE-2) / 0.654
3pyz ANPDihydrofolate synthase/folylpolyglutamate synthase / 0.654
4a1z ADPKinesin-like protein KIF11 / 0.654
4u0s ADPAdenosine monophosphate-protein transferase FICD 2.7.7.n1 0.654
1nly AGSCag alpha / 0.653
2gcp GSPRho-related GTP-binding protein RhoC / 0.653
2rgb GNPGTPase HRas / 0.653
3fwy ADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / 0.653
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.653
3tjz GNPADP-ribosylation factor 1 / 0.653
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.653
4y0v GDPADP-ribosylation factor 1, putative / 0.653
4ylg GDPADP-ribosylation factor 1, putative / 0.653
1kmq GNPTransforming protein RhoA / 0.652
3oiu GNPGTPase HRas / 0.652
1loo GTPAdenylosuccinate synthetase isozyme 1 / 0.651
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.651
2j5x GSPADP-ribosylation factor 6 / 0.651
3i3s GNPGTPase HRas / 0.651
3k8y GNPGTPase HRas / 0.651
3oiw GNPGTPase HRas / 0.651
4dlv GNPGTPase HRas / 0.651
4dlw GNPGTPase HRas / 0.651
4pk4 ADPUnconventional myosin-VI / 0.651
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.650
1xd9 ADPNitrogenase iron protein 1 1.18.6.1 0.650
1xkv ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.650
3lbh GNPGTPase HRas / 0.650
3rs0 GNPGTPase HRas / 0.650
3tso GNPRas-related protein Rab-25 / 0.650
3v4f GNPGTPase HRas / 0.650
4ww4 ADPRuvB-like helicase / 0.650
5b2z GNPGTPase HRas / 0.650
5d3q GDPDynamin-1 3.6.5.5 0.650
5dha GNPGTP-binding nuclear protein Ran / 0.650