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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
1khe GCP Phosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1khe GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 1.179
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.907
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.836
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.832
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.799
5jlj GNPGTP-binding nuclear protein Ran / 0.794
4dlw GNPGTPase HRas / 0.780
1k5d GNPGTP-binding nuclear protein Ran / 0.778
3tgp GNPGTPase HRas / 0.777
4kvg GTPRas-related protein Rap-1A / 0.777
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.775
1kmq GNPTransforming protein RhoA / 0.773
2ov2 GCPRas-related C3 botulinum toxin substrate 3 / 0.773
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.772
1aq2 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.769
1vg8 GNPRas-related protein Rab-7a / 0.769
2c5l GTPGTPase HRas / 0.769
3w3z GTPGTP-binding nuclear protein Ran / 0.768
1wdt GTPElongation factor G (EF-G-2) / 0.767
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.767
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.767
2qtv GNPSmall COPII coat GTPase SAR1 3.6.5 0.767
3lbn GNPGTPase HRas / 0.767
4xoi GTPTransforming protein RhoA / 0.765
5dif GNPGTP-binding nuclear protein Ran / 0.764
1g17 GNPRas-related protein SEC4 / 0.761
2j0s ANPEukaryotic initiation factor 4A-III 3.6.4.13 0.761
4uj3 GNPRas-related protein Rab-11A / 0.761
1zc3 GNPRas-related protein Ral-A / 0.757
1zc4 GNPRas-related protein Ral-A / 0.756
2rgb GNPGTPase HRas / 0.755
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.755
1f5n GNPGuanylate-binding protein 1 / 0.754
1tu3 GNPRas-related protein Rab-5A / 0.754
3oiu GNPGTPase HRas / 0.754
4hdo GNPRas-related protein Rap-1b / 0.754
2rgc GNPGTPase HRas / 0.753
4dlv GNPGTPase HRas / 0.753
4l9w GNPGTPase HRas / 0.753
5b2z GNPGTPase HRas / 0.753
3ddc GNPGTPase HRas / 0.752
3rab GNPRas-related protein Rab-3A / 0.752
3tkl GTPRas-related protein Rab-1A / 0.752
3tso GNPRas-related protein Rab-25 / 0.752
4dlt GNPGTPase HRas / 0.752
4dlx GNPGTPase HRas / 0.752
4dlz GNPGTPase HRas / 0.752
3kko GNPRas-related protein M-Ras / 0.751
3rs7 GNPGTPase HRas / 0.751
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.750
3m0e ATPTranscriptional regulator (NtrC family) / 0.749
3oiv GNPGTPase HRas / 0.749
3i3s GNPGTPase HRas / 0.748
1s1c GNPTransforming protein RhoA / 0.747
3kz1 GSPTransforming protein RhoA / 0.745
1a2b GSPTransforming protein RhoA / 0.744
1mh1 GNPRas-related C3 botulinum toxin substrate 1 / 0.744
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.744
3sqx ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.744
2gil GTPRas-related protein Rab-6A / 0.741
2rgg GNPGTPase HRas / 0.737
4dls GNPGTPase HRas / 0.737
2gcp GSPRho-related GTP-binding protein RhoC / 0.736
3k8y GNPGTPase HRas / 0.736
3x1z GNPRas-related protein Rap-1b / 0.736
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.736
5dha GNPGTP-binding nuclear protein Ran / 0.734
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.733
1uad GNPRas-related protein Ral-A / 0.733
1xtr GNPGTP-binding protein Rheb / 0.733
2bku GTPGTP-binding nuclear protein Ran / 0.733
3vhx GTPADP-ribosylation factor 6 / 0.733
3ez3 ZOLFarnesyl pyrophosphate synthase, putative / 0.732
3pit GNPRas-related protein M-Ras / 0.732
3sbd GNPRas-related C3 botulinum toxin substrate 1 / 0.732
1cxz GSPTransforming protein RhoA / 0.731
3sqw ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.731
4lhw GNPRas-related protein Rab-8A / 0.731
4xsg GSPTransforming protein RhoA / 0.731
3oes GNPGTPase RhebL1 / 0.730
4js0 GNPCell division control protein 42 homolog / 0.730
1p3d ANPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.729
1n6l GTPRas-related protein Rab-5A / 0.727
3eg5 GNPCell division control protein 42 homolog / 0.727
1yu9 GNPRas-related protein Rab-4A / 0.725
4idn GNPAtlastin-1 3.6.5 0.725
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.725
2ic5 GNPRas-related C3 botulinum toxin substrate 3 / 0.724
1rqj RISFarnesyl diphosphate synthase 2.5.1.10 0.723
3l8y GNPGTPase HRas / 0.723
3mjh GTPRas-related protein Rab-5A / 0.723
4dvg GSPRho family GTPase / 0.723
4k81 GTPGTPase HRas / 0.723
1u0h GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.722
3lbh GNPGTPase HRas / 0.722
4db1 ANPMyosin-7 / 0.722
1zbd GTPRas-related protein Rab-3A / 0.721
2rge GNPGTPase HRas / 0.721
3law GNPRas-related protein Rab-7a / 0.721
2cls GTPRho-related GTP-binding protein Rho6 / 0.720
3th5 GNPRas-related C3 botulinum toxin substrate 1 / 0.719
4h5c YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.719
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.719
2q3f GNPRas-related GTP-binding protein D / 0.717
4xvq GNPGTPase HRas / 0.717
4dwb 0M7Farnesyl pyrophosphate synthase / 0.716
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.714
2zev B71Geranylgeranyl pyrophosphate synthase / 0.714
3b1x GNPFerrous iron transport protein B / 0.713
2db3 ANPATP-dependent RNA helicase vasa, isoform A 3.6.4.13 0.712
3bc1 GNPRas-related protein Rab-27A / 0.712
1rqj IPEFarnesyl diphosphate synthase 2.5.1.10 0.711
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.711
1ibr GNPGTP-binding nuclear protein Ran / 0.710
1lfd GNPGTPase HRas / 0.710
1q3h ANPCystic fibrosis transmembrane conductance regulator / 0.710
2jlr ANPGenome polyprotein 3.4.21.91 0.710
3qbt GNPRas-related protein Rab-8A / 0.710
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.709
1am4 GNPCell division control protein 42 homolog / 0.706
1esn ANPPantothenate kinase 2.7.1.33 0.706
2cl6 CAGGTPase HRas / 0.706
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.706
3e5h GNPRas-related protein Rab-28 / 0.706
3k9l GNPGTPase HRas / 0.706
1fmw ATPMyosin-2 heavy chain / 0.704
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.704
4g0n GNPGTPase HRas / 0.704
4kln AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.704
4idp GNPAtlastin-1 3.6.5 0.703
1gqy ACPUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.701
4dxj 0M9Farnesyl pyrophosphate synthase / 0.701
4tle AGSCircadian clock protein kinase KaiC 2.7.11.1 0.701
4xvr GNPGTPase HRas / 0.701
4goj GNPADP-ribosylation factor-like protein 3 / 0.700
1m7b GTPRho-related GTP-binding protein RhoE / 0.699
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.698
2bif ANP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.698
4kqs RISFarnesyl pyrophosphate synthase 2.5.1.10 0.698
3hu2 AGSTransitional endoplasmic reticulum ATPase 3.6.4.6 0.697
4gzl GNPRas-related C3 botulinum toxin substrate 1 / 0.696
4tlb AGSCircadian clock protein kinase KaiC 2.7.11.1 0.696
3oeh ANPATP synthase subunit alpha, mitochondrial / 0.695
4ol0 GTPGTP-binding nuclear protein Ran / 0.695
3rye UNRFarnesyl pyrophosphate synthase 2.5.1.10 0.694
4dem YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.694
5di3 GNPADP-ribosylation factor-like protein 3 / 0.692
3n0z 3ATAdenylate cyclase 2 / 0.691
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.691
4d0l GSPRas-related protein Rab-11A / 0.689
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.689
3a58 GNPGTP-binding protein RHO1 / 0.688
3hqd ANPKinesin-like protein KIF11 / 0.688
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.688
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.683
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.678
4nyi GNPGTPase HRas / 0.677
4q23 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.677
4v02 ATPSite-determining protein / 0.677
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.676
2bkk ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.676
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.676
3pcr GTPADP-ribosylation factor 6 / 0.676
4cvl ACPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / 0.676
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.676
2w2x GSPRas-related C3 botulinum toxin substrate 2 / 0.675
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.675
1bif AGS6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 2.7.1.105 0.674
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.672
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.672
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA2 3.6.3 0.672
4zir ANPEnergy-coupling factor transporter ATP-binding protein EcfA1 / 0.672
1oe0 TTPDeoxynucleoside kinase / 0.671
1rj9 GCPSignal recognition particle receptor FtsY / 0.671
4dee ADPAurora kinase A 2.7.11.1 0.671
3r9x GNPGTPase Era / 0.669
3ryh GTPTubulin alpha chain / 0.669
1z2c GNPRho-related GTP-binding protein RhoC / 0.668
2c96 ATPPsp operon transcriptional activator / 0.668
4tl8 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.668
4wpu GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.666
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.665
2jj1 ANPATP synthase subunit alpha, mitochondrial / 0.665
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.664
1wbb ADPDNA mismatch repair protein MutS / 0.663
2e95 B75Geranylgeranyl pyrophosphate synthase / 0.663
2z4z SC0Geranylgeranyl pyrophosphate synthase / 0.663
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.663
4nke IPEFarnesyl pyrophosphate synthase 2.5.1.10 0.663
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.662
3ryw K9HFarnesyl pyrophosphate synthase, putative / 0.662
4bzq ADPBifunctional enzyme CysN/CysC 2.7.1.25 0.662
4h5e YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.662
4lfv YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.662
1lwx AZDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.661
1z5c ADPType 2 DNA topoisomerase 6 subunit B / 0.661
5la6 GTPTubulin alpha-1B chain / 0.661
4h5d YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.660
1l8t ADPAminoglycoside 3'-phosphotransferase 2.7.1.95 0.659
4l2x YL2Farnesyl pyrophosphate synthase 2.5.1.10 0.659
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.658
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.658
4ceg ADPAurora kinase A 2.7.11.1 0.658
3w2w ATPCRISPR system Cmr subunit Cmr2 / 0.657
1w5t ADPORC1-type DNA replication protein 2 / 0.656
4ohv ANPProtein clpf-1 / 0.656
2ck3 ANPATP synthase subunit alpha, mitochondrial / 0.655
2ck3 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.655
3dyh 721Farnesyl pyrophosphate synthase / 0.655
4jvj 1MVFarnesyl pyrophosphate synthase 2.5.1.10 0.655
4uj5 GNPRas-related protein Rab-11A / 0.654
5c46 GSPRas-related protein Rab-11A / 0.654
2qme GCPRas-related C3 botulinum toxin substrate 3 / 0.652
4bri UNPEctonucleoside triphosphate diphosphohydrolase I / 0.652
4dxa GSPRas-related protein Rap-1b / 0.652
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.652
1szg FNSCytochrome b2, mitochondrial 1.1.2.3 0.651
1tys TMPThymidylate synthase / 0.651
4ork GDPBifunctional AAC/APH 2.3.1 0.651
1a5u ATPPyruvate kinase PKM 2.7.1.40 0.650