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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
4prxADPDNA gyrase subunit B

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4prxADPDNA gyrase subunit B/1.000
4wucANPDNA gyrase subunit B/0.660
4wudANPDNA gyrase subunit B/0.645
4prvADPDNA gyrase subunit B/0.641
1ei1ANPDNA gyrase subunit B/0.514
3zkbANPDNA gyrase subunit B/0.501
3u33FADPutative acyl-CoA dehydrogenase AidB1.3.990.491
2a94AP0L-lactate dehydrogenase1.1.1.270.483
4ipeANPTNF receptor-associated protein 1/0.483
2hrcCHDFerrochelatase, mitochondrial4.99.1.10.472
1nhhANPDNA mismatch repair protein MutL/0.471
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.471
2z4sADPChromosomal replication initiator protein DnaA/0.469
1yb5NAPQuinone oxidoreductase1.6.5.50.468
2zdyADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.466
1i24UPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.465
2vd0D27Hematopoietic prostaglandin D synthase/0.465
5ar4SB2Receptor-interacting serine/threonine-protein kinase 22.7.11.10.465
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.464
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.463
2e0aANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.463
3f3sNADLambda-crystallin homolog/0.463
3zkdANPDNA gyrase subunit B/0.463
1eioGCHGastrotropin/0.462
2zkjADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.461
4ejn0R4RAC-alpha serine/threonine-protein kinase2.7.11.10.461
1i59ADPChemotaxis protein CheA2.7.13.30.460
4l0qNADAlcohol dehydrogenase class-3/0.460
1zxmANPDNA topoisomerase 2-alpha5.99.1.30.458
1fm4DXCMajor pollen allergen Bet v 1-L/0.457
3d2rADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.457
3owaFADAcyl-CoA dehydrogenase/0.457
5dp2NAPCurF/0.455
1me6IVSPlasmepsin-23.4.23.390.454
1rx0FADIsobutyryl-CoA dehydrogenase, mitochondrial1.3.990.454
1xddAAYIntegrin alpha-L/0.454
1xe55FEPlasmepsin-23.4.23.390.451
2gjlFMNNitronate monooxygenase1.13.12.160.451
1qorNDPQuinone oxidoreductase 1/0.450
1egeFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.449
1xkdNAPIsocitrate dehydrogenase [NADP]/0.449
3pefNAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase/0.449
3sf6FDAGlutaryl-CoA dehydrogenase/0.449
4f9fGDPPutative glycosyltransferase/0.449
4g7gVFVLanosterol 14-alpha-demethylase/0.449
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.449
1tqf32PBeta-secretase 13.4.23.460.448
2dvlFADAcyl-CoA dehydrogenase/0.448
1t2cNAIL-lactate dehydrogenase1.1.1.270.447
1i5cADPChemotaxis protein CheA2.7.13.30.446
1i59ANPChemotaxis protein CheA2.7.13.30.445
2xhrC0PHeat shock protein HSP 90-alpha/0.445
3sl2ATPSensor histidine kinase WalK/0.445
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.445
1lbcCYZGlutamate receptor 2/0.444
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.444
2oapANPType II secretion system protein (GspE-2)/0.444
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.444
4g3jVNTLanosterol 14-alpha-demethylase/0.444
1dr3TAPDihydrofolate reductase1.5.1.30.443
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.443
4ambDUDPutative glycosyl transferase/0.443
4bfzZVZPantothenate kinase2.7.1.330.443
4u0mGTPCyclic GMP-AMP synthase/0.443
4y9qC2EUncharacterized protein/0.443
2d1cNAPIsocitrate dehydrogenase [NADP]1.1.1.420.442
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.442
5hwsNAP2-dehydropantoate 2-reductase/0.442
1rsgFADPolyamine oxidase FMS1/0.441
2e83FMNFMN-binding protein/0.441
2mwgFMNBlue-light photoreceptor/0.441
3uovFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.441
4a6nFADTetX family tetracycline inactivation enzyme/0.441
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
4y93746Tyrosine-protein kinase/0.441
1okkGCPSignal recognition particle protein/0.440
1okkGCPSignal recognition particle receptor FtsY/0.440
1qrrUPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.440
1um0FMNChorismate synthase/0.440
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.440
4ipw1G7Mycocyclosin synthase1.14.21.90.440