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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
5cyp GSP Septin-9

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5cyp GSPSeptin-9 / 1.032
4yqf GDPSeptin-9 / 0.776
1eyn 2ANUDP-N-acetylglucosamine 1-carboxyvinyltransferase / 0.744
2xvv 9DNSerum albumin / 0.744
3cz0 9ODPheromone-binding protein ASP1 / 0.744
3fo7 IMNPhospholipase A2 VRV-PL-VIIIa / 0.744
3nfa CBJGag-Pol polyprotein / 0.744
3ngq 1PSCCR4-NOT transcription complex subunit 6-like 3.1.13.4 0.744
3nks ACJProtoporphyrinogen oxidase 1.3.3.4 0.744
4dsb A8SAbscisic acid receptor PYL3 / 0.744
4ivo ACJProtoporphyrinogen oxidase 1.3.3.4 0.744
4kla CHDFerrochelatase, mitochondrial 4.99.1.1 0.744
5dby DIFSerum albumin / 0.744
5dby NPSSerum albumin / 0.744
4m0l GDPTranslation initiation factor 2 subunit gamma / 0.738
4z54 GDPNeuronal-specific septin-3 / 0.725
3ftq GNPSeptin-2 / 0.717
3onw GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.716
1gil GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.714
1zcb GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.714
2ffq GSPRas-related protein Rab-6B / 0.713
4oi2 ADPProtein clpf-1 / 0.713
2gil GTPRas-related protein Rab-6A / 0.710
3kkq GDPRas-related protein M-Ras / 0.708
2v7q ATPATP synthase subunit alpha, mitochondrial / 0.707
2v7q ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.707
1t91 GTPRas-related protein Rab-7a / 0.705
4pao GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.704
3cx6 GDPGuanine nucleotide-binding protein subunit alpha-13 / 0.700
3cx8 GSPGuanine nucleotide-binding protein subunit alpha-13 / 0.700
4pan GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.700
1h65 GDPTranslocase of chloroplast 34 3.6.5 0.699
1z0d GDPRas-related protein Rab-5C / 0.699
4dsu GDPGTPase KRas / 0.698
5cyo GDPSeptin-9 / 0.698
5hpy GDPTransforming protein RhoA / 0.698
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.695
2xtz GSPGuanine nucleotide-binding protein alpha-1 subunit / 0.695
4qxa GTPRas-related protein Rab-9A / 0.695
4asu ADPATP synthase subunit alpha, mitochondrial / 0.694
4g5q GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.694
1tu3 GNPRas-related protein Rab-5A / 0.693
2g0n GDPRas-related C3 botulinum toxin substrate 3 / 0.693
4epw GDPGTPase KRas / 0.693
4idn GNPAtlastin-1 3.6.5 0.693
2ic5 GDPRas-related C3 botulinum toxin substrate 3 / 0.692
3b1x GNPFerrous iron transport protein B / 0.692
4epx GDPGTPase KRas / 0.692
4tq9 GDPGTPase KRas / 0.692
1w0k ADPATP synthase subunit alpha, mitochondrial / 0.691
1w0k ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.691
2dpx GDPGTP-binding protein RAD / 0.691
3a6p GTPGTP-binding nuclear protein Ran / 0.690
1a2b GSPTransforming protein RhoA / 0.689
4lhv GDPRas-related protein Rab-8A / 0.689
4q02 GDPGTPase KRas / 0.689
3law GNPRas-related protein Rab-7a / 0.686
4g0n GNPGTPase HRas / 0.686
4r43 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.686
3sop GDPNeuronal-specific septin-3 / 0.685
5dha GNPGTP-binding nuclear protein Ran / 0.684
1gp2 GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.683
2fna ADPUncharacterized protein / 0.683
3bb3 GDPTranslocase of chloroplast 33, chloroplastic 3.6.5 0.683
4nh0 ATPESX secretion system protein EccC / 0.682
5dif GNPGTP-binding nuclear protein Ran / 0.682
1cul GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.680
1xmv ADPProtein RecA / 0.680
1z2a GDPRas-related protein Rab-23 / 0.680
2ce2 GDPGTPase HRas / 0.680
2fe4 GDPRas-related protein Rab-6B / 0.680
3x1w GDPRas-related protein Rap-1b / 0.680
4dvg GSPRho family GTPase / 0.680
1x1r GDPRas-related protein M-Ras / 0.679
2bku GTPGTP-binding nuclear protein Ran / 0.679
1e79 ATPATP synthase subunit alpha, mitochondrial / 0.678
1e79 ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.678
4ldj GDPGTPase KRas / 0.678
2p2l GDPRas-related C3 botulinum toxin substrate 1 / 0.677
3vhx GTPADP-ribosylation factor 6 / 0.677
4lrw GDPGTPase KRas / 0.677
4y0v GDPADP-ribosylation factor 1, putative / 0.677
4ylg GDPADP-ribosylation factor 1, putative / 0.677
1cs4 GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.676
1oix GDPRas-related protein Rab-11A / 0.676
2gvd GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.676
4kvg GTPRas-related protein Rap-1A / 0.676
1wdt GTPElongation factor G (EF-G-2) / 0.675
3oes GNPGTPase RhebL1 / 0.675
4xoi GTPTransforming protein RhoA / 0.675
1wbb ADPDNA mismatch repair protein MutS / 0.674
4cym GCPRas-related protein Rab-32 / 0.674
4q03 GDPGTPase KRas / 0.674
4xsg GSPTransforming protein RhoA / 0.674
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.673
2iut AGSDNA translocase FtsK / 0.673
2jiz ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.673
2pg2 ADPKinesin-like protein KIF11 / 0.673
3ref GDPRho family GTPase / 0.673
1f5n GNPGuanylate-binding protein 1 / 0.672
4oi4 ATPmRNA cleavage and polyadenylation factor CLP1 / 0.672
2w2v GTPRas-related C3 botulinum toxin substrate 2 / 0.671
2x7e ADPKinesin-like protein KIF11 / 0.671
3rab GNPRas-related protein Rab-3A / 0.671
3r9i ADPSeptum site-determining protein MinD / 0.669
3w3z GTPGTP-binding nuclear protein Ran / 0.669
3moh GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.668
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.668
1w5t ANPORC1-type DNA replication protein 2 / 0.667
1w5t ADPORC1-type DNA replication protein 2 / 0.666
1zd9 GDPADP-ribosylation factor-like protein 8A / 0.666
2qen ADPWalker-Type ATPase / 0.666
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.666
3ea5 GDPGTP-binding nuclear protein Ran / 0.666
4tla ADPCircadian clock protein kinase KaiC 2.7.11.1 0.666
4zca ADPKinesin-like protein KIF11 / 0.666
1got GDPGuanine nucleotide-binding protein G(t) subunit alpha-1 / 0.665
2zfi ADPKinesin-like protein KIF1A / 0.665
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.665
1bof GDPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.664
2gm1 ADPKinesin-like protein KIF11 / 0.664
2xau ADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 3.6.4.13 0.664
3mjh GTPRas-related protein Rab-5A / 0.664
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 0.664
4d0l GSPRas-related protein Rab-11A / 0.664
4itr GDPCell division control protein 42 homolog / 0.664
5aun ADPIron-sulfur cluster carrier protein / 0.664
1e96 GTPRas-related C3 botulinum toxin substrate 1 / 0.663
1z0f GDPRas-related protein Rab-14 / 0.663
2q3f GNPRas-related GTP-binding protein D / 0.663
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.663
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.662
2hf8 GSPProbable hydrogenase nickel incorporation protein HypB / 0.662
2zet GTPRas-related protein Rab-27B / 0.662
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.662
4lpk GDPGTPase KRas / 0.662
4wou GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.662
5bn3 ADPV-type ATP synthase alpha chain / 0.662
5bn3 ADPNEQ263 / 0.662
1jx2 ADPMyosin-2 heavy chain / 0.661
2c5l GTPGTPase HRas / 0.661
2jj2 ADPATP synthase subunit alpha, mitochondrial / 0.661
2jj2 ADPATP synthase subunit beta, mitochondrial 3.6.3.14 0.661
3wyf GTPGTP-binding nuclear protein / 0.661
4ihq ADPConserved Archaeal protein / 0.661
4pfp ADPUnconventional myosin-VI / 0.661
1rml NTSFibroblast growth factor 1 / 0.660
1sa4 JANProtein farnesyltransferase subunit beta 2.5.1.58 0.660
2f0y 3MNProtein farnesyltransferase subunit beta 2.5.1.58 0.660
2iej S48Protein farnesyltransferase subunit beta 2.5.1.58 0.660
2j5x GSPADP-ribosylation factor 6 / 0.660
2l0x GDPGTP-binding protein Rheb / 0.660
2qd3 CHDFerrochelatase, mitochondrial 4.99.1.1 0.660
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.660
3k14 5352-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 0.660
3ksq Z96Protein farnesyltransferase subunit beta 2.5.1.58 0.660
3o3j BB4Peptide deformylase 1B, chloroplastic/mitochondrial 3.5.1.88 0.660
3pz3 PZ3Geranylgeranyl transferase type-2 subunit beta 2.5.1.60 0.660
3pz4 3PZProtein farnesyltransferase subunit beta 2.5.1.58 0.660
3sfx JANUncharacterized protein / 0.660
3znr NU9Histone deacetylase 7 3.5.1.98 0.660
4lnb ED5CaaX farnesyltransferase beta subunit Ram1 / 0.660
4lng JANCaaX farnesyltransferase beta subunit Ram1 / 0.660
4obe GDPGTPase KRas / 0.660
5kcp PFBAlcohol dehydrogenase E chain 1.1.1.1 0.660
1cxz GSPTransforming protein RhoA / 0.659
1ky2 GNPGTP-binding protein YPT7 / 0.659
1t47 NTD4-hydroxyphenylpyruvate dioxygenase 1.13.11.27 0.659
4gp6 ADPMetallophosphoesterase / 0.659
5di3 GNPADP-ribosylation factor-like protein 3 / 0.659
1ohh ANPATP synthase subunit alpha, mitochondrial / 0.658
1ohh ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.658
1sqi 8694-hydroxyphenylpyruvate dioxygenase / 0.658
1xef ATPAlpha-hemolysin translocation ATP-binding protein HlyB / 0.658
3cob ADPKinesin heavy chain-like protein / 0.658
4a1z ADPKinesin-like protein KIF11 / 0.658
4qos ADPPsp operon transcriptional activator / 0.658
1yzq GNPRas-related protein Rab-6A / 0.657
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.657
3fkq ATPNtrC-like two-domain protein / 0.657
3tqc ADPPantothenate kinase / 0.657
4dso GSPGTPase KRas / 0.657
2gcp GSPRho-related GTP-binding protein RhoC / 0.656
2y65 ADPKinesin heavy chain / 0.656
3c41 ANPAmino acid ABC transporter / 0.656
4jl6 ADPAdenylate kinase / 0.656
4uj3 GNPRas-related protein Rab-11A / 0.656
5da9 AGSUncharacterized protein / 0.656
1azt GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short / 0.655
1n6l GTPRas-related protein Rab-5A / 0.655
1ow3 GDPTransforming protein RhoA / 0.655
1z2c GNPRho-related GTP-binding protein RhoC / 0.655
2cl6 CAGGTPase HRas / 0.655
3pcn DHYProtocatechuate 3,4-dioxygenase alpha chain 1.13.11.3 0.655
3pcn DHYProtocatechuate 3,4-dioxygenase beta chain 1.13.11.3 0.655
3t1t GDPProbable gliding protein mglA / 0.654
3tgp GNPGTPase HRas / 0.654
3zvm ADPBifunctional polynucleotide phosphatase/kinase 2.7.1.78 0.654
4jld ADPAdenylate kinase / 0.654
5jlj GNPGTP-binding nuclear protein Ran / 0.654
2j0v GDPRac-like GTP-binding protein ARAC7 / 0.653
4ncl GDPEukaryotic translation initiation factor 5B / 0.653
1sdm ADPKinesin heavy chain-like protein / 0.652
2zts ADPUncharacterized protein / 0.652
3fmo ADPATP-dependent RNA helicase DDX19B 3.6.4.13 0.652
4jky ADPAdenylate kinase / 0.652
4o2r GDPGTP-binding protein Rheb / 0.652
1z0a GDPRas-related protein Rab-2A / 0.651
2i1v ADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.651
4ike ADPAdenylate kinase / 0.651
4l9s GDPGTPase HRas / 0.651
4lv6 GDPGTPase KRas / 0.651
5c46 GSPRas-related protein Rab-11A / 0.651
1fnn ADPORC1-type DNA replication protein / 0.650
1xtr GNPGTP-binding protein Rheb / 0.650
4cf7 ADPAdenylate kinase / 0.650
4o2l GTPGTP-binding protein Rheb / 0.650
4ql3 GDPGTPase KRas / 0.650
4xvr GNPGTPase HRas / 0.650