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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
1rrgGDPADP-ribosylation factor 1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1rrgGDPADP-ribosylation factor 1/1.000
4ylgGDPADP-ribosylation factor 1, putative/0.604
4y0vGDPADP-ribosylation factor 1, putative/0.603
4fduIHSPutative multiple inositol polyphosphate histidine phosphatase 1/0.512
3lm8VIBThiamine pyrophosphokinase2.7.6.20.502
1sesAHXSerine--tRNA ligase6.1.1.110.500
2briANPUridylate kinase2.7.4.220.500
4blsAPCNTPase P4/0.487
1jdtMTAPurine nucleoside phosphorylase/0.486
2f3rG5PGuanylate kinase2.7.4.80.486
3c4vLIPD-inositol 3-phosphate glycosyltransferase2.4.1.2500.486
4hyvPEPPyruvate kinase 12.7.1.400.486
4loi1YCStimulator of interferon genes protein/0.485
3ihkTPPUncharacterized protein/0.484
3opmLUIDipeptidyl peptidase 4/0.481
2xfsJ01Uncharacterized protein/0.480
2uz3TTPThymidine kinase/0.479
2ylrNAPPhenylacetone monooxygenase1.14.13.920.479
4hmvWUBPhenazine biosynthesis protein PhzG1.40.478
1w5tADPORC1-type DNA replication protein 2/0.477
2w02ATPAcsD/0.477
3ceaNADMyo-inositol 2-dehydrogenase-like (Promiscuous)/0.477
3h4vNAPPteridine reductase 11.5.1.330.477
4r1lADPPhenylacetate-coenzyme A ligase/0.476
5bt9NAP3-oxoacyl-(Acyl-carrier-protein) reductase/0.476
2freFMNNAD(P)H-flavin oxidoreductase/0.474
3kjiADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.474
3tr05GPGuanylate kinase/0.473
3ea0ATPATPase, ParA family/0.472
4fj2NAP17beta-hydroxysteroid dehydrogenase/0.472
1szfFMNCytochrome b2, mitochondrial1.1.2.30.471
1i3lGDUUDP-glucose 4-epimerase/0.470
1p4aPCPPur operon repressor/0.470
5ftcADPTPR domain protein/0.469
3fccATPD-alanine--poly(phosphoribitol) ligase subunit 1/0.468
4m2aUPGUDP-glucose pyrophosphorylase/0.467
1w5tANPORC1-type DNA replication protein 2/0.465
2aj8SC3Dipeptidyl peptidase 4/0.465
4ihjGTPTubulin alpha-1B chain/0.465
1nj6A5AProline--tRNA ligase/0.463
1u80C5PCoenzyme A biosynthesis bifunctional protein CoaBC6.3.2.50.463
2gn4UD1UDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.463
4iokADPFormate--tetrahydrofolate ligase/0.462
1kqcFMNOxygen-insensitive NAD(P)H nitroreductase/0.461
2eudGCQRibonucleoside-diphosphate reductase large chain 11.17.4.10.461
3tjzGNPADP-ribosylation factor 1/0.461
3udq09EBeta-secretase 13.4.23.460.461
1s4eADPGalactokinase/0.460
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.460
3q4zANPSerine/threonine-protein kinase PAK 12.7.11.10.460
3x2uATPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.460
5a04NDPGlucose-fructose oxidoreductase/0.460
1n2eAPCPantothenate synthetase6.3.2.10.459
3fhyATPPyridoxal kinase2.7.1.350.459
1nj5P5AProline--tRNA ligase/0.458
1oonFMNOxygen-insensitive NAD(P)H nitroreductase/0.458
1guhGSBGlutathione S-transferase A12.5.1.180.457
1iqrFADDeoxyribodipyrimidine photo-lyase4.1.99.30.457
1rfvADPPyridoxal kinase2.7.1.350.457
3fceATPD-alanine--poly(phosphoribitol) ligase subunit 1/0.457
4xb1NDP319aa long hypothetical homoserine dehydrogenase/0.457
1goxFMNPeroxisomal (S)-2-hydroxy-acid oxidase1.1.3.150.456
3ccc7ACDipeptidyl peptidase 4/0.456
5agaANPDNA polymerase theta/0.456
3keuATPPyridoxal kinase2.7.1.350.455
4cojCTPUncharacterized protein/0.455
4o4iGTPTubulin alpha-1B chain/0.455
1jedADPSulfate adenylyltransferase/0.454
2bmbPMMFolic acid synthesis protein FOL1/0.454
3qw4U5POrotidine-5-phosphate decarboxylase/orotate phosphoribosyltransferase, putative/0.454
1p52ADPArginine kinase2.7.3.30.453
2qbuSAHPrecorrin-2 methyltransferase/0.453
3hu2AGSTransitional endoplasmic reticulum ATPase3.6.4.60.453
3hyoADPPyridoxal kinase/0.453
4c13UMLUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase/0.453
4cloNAPPteridine reductase/0.453
4nesUD1UDP-N-acetylglucosamine 2-epimerase5.1.3.140.453
5a0yCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.453
5a0yCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.453
1lrjUD1UDP-glucose 4-epimerase5.1.3.20.452
2dftADPShikimate kinase2.7.1.710.452
3muoZPRProlyl endopeptidase/0.452
3v0o4GWHisto-blood group ABO system transferase/0.452
4auxXTCTetracycline repressor protein class D/0.452
4bio8XQHypoxia-inducible factor 1-alpha inhibitor1.14.11.300.452
5bsmATP4-coumarate--CoA ligase 26.2.1.120.452
1oo5FMNOxygen-insensitive NAD(P)H nitroreductase/0.451
2yxuATPPyridoxal kinase2.7.1.350.451
3pgtGBXGlutathione S-transferase P2.5.1.180.451
3ta1ADPNitrogen regulatory protein P-II (GlnB-3)/0.450
3w1tWRODihydroorotate dehydrogenase (fumarate)1.3.98.10.450
1yidATPTryptophan--tRNA ligase 26.1.1.20.449
2dknNAI3-alpha-hydroxysteroid dehydrogenase/0.449
1n2gAPCPantothenate synthetase6.3.2.10.448
2r8fAGSNon-structural protein 23.6.40.448
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.448
4h9tHL4Phosphotriesterase/0.448
1pgtGTXGlutathione S-transferase P2.5.1.180.447
2q14ADPPhosphohydrolase/0.447
2yw2ATPPhosphoribosylamine--glycine ligase/0.447
4lol1YEStimulator of interferon genes protein/0.447
5a02NAPGlucose-fructose oxidoreductase/0.447
5fklTDCTetracycline repressor protein class D/0.447
1kqdFMNOxygen-insensitive NAD(P)H nitroreductase/0.446
1u1gBBBUridine phosphorylase2.4.2.30.446
2gn6UD1UDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.446
2vhzNAIAlanine dehydrogenase1.4.1.10.446
3w1rMRODihydroorotate dehydrogenase (fumarate)1.3.98.10.446
5a06NDPGlucose-fructose oxidoreductase/0.446
1dxyNADD-2-hydroxyisocaproate dehydrogenase1.1.10.445
1qbqHFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.445
1qbqHFPProtein farnesyltransferase subunit beta2.5.1.580.445
1s4oGDPGlycolipid 2-alpha-mannosyltransferase/0.445
1vl8NAPOxidoreductase, short chain dehydrogenase/reductase family/0.445
1xmvADPProtein RecA/0.445
2xb5I7TTetracycline repressor protein class D/0.445
2xtzGSPGuanine nucleotide-binding protein alpha-1 subunit/0.445
3ivmZPRProlyl endopeptidase/0.445
3wqmB29Diterpene synthase3.1.7.80.445
4avlTMPPolymerase acidic protein/0.445
4s26SAHPhosphomethylpyrimidine synthase, chloroplastic4.1.99.170.445
4zm3PLPAminotransferase/0.445
1nl4HFPProtein farnesyltransferase subunit beta2.5.1.580.444
1vfrFMNMajor NAD(P)H-flavin oxidoreductase1.6.990.444
2g89UMPThymidylate synthase/0.444
2r7pANPNon-structural protein 23.6.40.444
2ydxNAPMethionine adenosyltransferase 2 subunit beta/0.444
3hf3FMNChromate reductase/0.444
3phcIM5Purine nucleoside phosphorylase/0.444
4en4ATPPyridoxal kinase2.7.1.350.444
4eo3FMNBacterioferritin comigratory protein/NADH dehydrogenase/0.444
4ohwATPProtein clpf-1/0.444
4qxp1YEStimulator of interferon genes protein/0.444
1i59ANPChemotaxis protein CheA2.7.13.30.443
1icvFMNOxygen-insensitive NAD(P)H nitroreductase/0.443
1noiNTZGlycogen phosphorylase, muscle form2.4.1.10.443
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.443
1wc1TATAdenylate cyclase/0.443
3elbC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.443
3g8cADPBiotin carboxylase6.3.4.140.443
4ac0MIYTetracycline repressor protein class B from transposon Tn10/0.443
4jjzADPFormate--tetrahydrofolate ligase/0.443
5ayzNCNNicotinate-nucleotide pyrophosphorylase [carboxylating]2.4.2.190.443
5jsfNAD17-beta-hydroxysteroid dehydrogenase 141.1.10.443
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.442
1towCRZFatty acid-binding protein, adipocyte/0.442
3c212BADNA integrity scanning protein DisA/0.442
3intGDUUDP-galactopyranose mutase5.4.99.90.442
3ptzNADUDP-glucose 6-dehydrogenase1.1.1.220.442
3r9iADPSeptum site-determining protein MinD/0.442
3zl8ADPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.442
4xj3GTPCyclic GMP-AMP synthase/0.442
1fyfSSAThreonine--tRNA ligase6.1.1.30.441
1ooqFMNOxygen-insensitive NAD(P)H nitroreductase/0.441
1ykiFMNOxygen-insensitive NAD(P)H nitroreductase/0.441
1z48FMNNADPH dehydrogenase/0.441
3jszUPGUncharacterized protein/0.441
1gz4ATPNAD-dependent malic enzyme, mitochondrial1.1.1.380.440
1kp2ATPArgininosuccinate synthase6.3.4.50.440
1szgFNSCytochrome b2, mitochondrial1.1.2.30.440
2b69NADUDP-glucuronic acid decarboxylase 14.1.1.350.440
2pb2PLPAcetylornithine/succinyldiaminopimelate aminotransferase2.6.1.110.440
2xrlDXTTetracycline repressor protein class D/0.440
2zsaADPPantothenate kinase2.7.1.330.440
3koyZ97D-ornithine 4,5-aminomutase subunit beta/0.440
3m2uCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.440
3rv8RVCSalicylate synthase/0.440
3tqcADPPantothenate kinase/0.440
3x22FMNOxygen-insensitive NAD(P)H nitroreductase/0.440
4fj1NAP17beta-hydroxysteroid dehydrogenase/0.440
4jc51K5Stimulator of interferon genes protein/0.440
4m2bUPGUDP-glucose pyrophosphorylase/0.440
4yvz3ATDNA integrity scanning protein DisA/0.440
4zolGTPTubulin alpha-1B chain/0.440