Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
4ywjNAD4-hydroxy-tetrahydrodipicolinate reductase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4ywjNAD4-hydroxy-tetrahydrodipicolinate reductase/1.000
5eesNAP4-hydroxy-tetrahydrodipicolinate reductase/0.579
2zs9ADPPantothenate kinase2.7.1.330.511
1yl7NAI4-hydroxy-tetrahydrodipicolinate reductase/0.508
4f5dC2EStimulator of interferon genes protein/0.508
1vfrFMNMajor NAD(P)H-flavin oxidoreductase1.6.990.500
4qak2AMRNA 2',3'-cyclic phosphodiesterase/0.489
3gg2UGASugar dehydrogenase, UDP-glucose/GDP-mannose dehydrogenase family/0.485
4ifn12OKelch-like ECH-associated protein 1/0.480
2r2nKYNKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.479
4jdcNADProbable pyrroline-5-carboxylate dehydrogenase RocA/0.476
3af0GDPPantothenate kinase2.7.1.330.475
4d6qPD2Lysine-specific demethylase 4D1.14.110.474
1kqbFMNOxygen-insensitive NAD(P)H nitroreductase/0.473
3nlzH4BNitric oxide synthase, brain1.14.13.390.473
1h6cNDPGlucose--fructose oxidoreductase1.1.99.280.470
1n0sFLUBilin-binding protein/0.470
3af1GDPPantothenate kinase2.7.1.330.470
4g0k0VSGlutathionyl-hydroquinone reductase YqjG1.80.470
1f9aATPNicotinamide-nucleotide adenylyltransferase/0.469
2culFADGidA-related protein/0.468
2gesCOKPantothenate kinase2.7.1.330.468
2geuCOKPantothenate kinase2.7.1.330.467
3qiyQI1Botulinum neurotoxin type A3.4.24.690.467
1h6bNDPGlucose--fructose oxidoreductase1.1.99.280.466
2h63NAPBiliverdin reductase A1.3.1.240.466
2hayFMNPutative NAD(P)H-flavin oxidoreductase/0.466
1sirNBCGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.465
4fa30SLAldo-keto reductase family 1 member C3/0.465
1oo5FMNOxygen-insensitive NAD(P)H nitroreductase/0.464
3zkyWT4Isopenicillin N synthase1.21.3.10.464
4loh1SYStimulator of interferon genes protein/0.464
4imtH4BNitric oxide synthase, brain1.14.13.390.463
3hf3FMNChromate reductase/0.462
4euxH4BNitric oxide synthase, brain1.14.13.390.462
4yp12BAStimulator of interferon genes protein/0.461
1hb1OCVIsopenicillin N synthase1.21.3.10.460
1m9nAMZBifunctional purine biosynthesis protein PURH2.1.2.30.460
1sesAHXSerine--tRNA ligase6.1.1.110.460
1zzuH4BNitric oxide synthase, brain1.14.13.390.460
3rqjH4BNitric oxide synthase, brain1.14.13.390.460
1hb3SCVIsopenicillin N synthase1.21.3.10.459
2hx4H4BNitric oxide synthase, brain1.14.13.390.459
3b3nH4BNitric oxide synthase, brain1.14.13.390.459
3frc0HGGlutathione S-transferase2.5.1.180.459
5cflC2EStimulator of interferon genes protein/0.459
3pzcCOAAmino acid--[acyl-carrier-protein] ligase 16.2.1.n20.458
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.457
2oo5TXDNAD(P) transhydrogenase subunit alpha part 11.6.1.20.457
3jxeTYMTryptophan--tRNA ligase/0.457
3tdkUPGUDP-glucose 6-dehydrogenase1.1.1.220.457
1nj5P5AProline--tRNA ligase/0.456
2p9cNAID-3-phosphoglycerate dehydrogenase1.1.1.950.456
3m2tNADProbable dehydrogenase/0.456
1n4qLYS_CYS_VAL_ILE_LEUGeranylgeranyl transferase type-1 subunit beta2.5.1.590.455
2hq9FADMll6688 protein/0.455
2r2lPB9Protein farnesyltransferase subunit beta2.5.1.580.455
3jt4H4BNitric oxide synthase, brain1.14.13.390.455
3nlnH4BNitric oxide synthase, brain1.14.13.390.455
4k36SAMAnaerobic sulfatase-maturating enzyme1.8.980.455
4qbiAP5Adenylate kinase/0.455
1h6dNDPGlucose--fructose oxidoreductase1.1.99.280.454
3e32ED2Protein farnesyltransferase subunit beta2.5.1.580.454
3jq3ADPLombricine kinase/0.454
4fvyH4BNitric oxide synthase, brain1.14.13.390.454
2obxINI6,7-dimethyl-8-ribityllumazine synthase 22.5.1.780.453
3x21FMNOxygen-insensitive NAD(P)H nitroreductase/0.453
4in44IDKelch-like ECH-associated protein 1/0.453
1ikgREXD-alanyl-D-alanine carboxypeptidase3.4.16.40.452
1re0AFBADP-ribosylation factor 1/0.452
1re0AFBARF guanine-nucleotide exchange factor 1/0.452
3ntrNADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase1.1.1.180.452
3pnfH4BNitric oxide synthase, brain1.14.13.390.452
4r20AERCytochrome P450 family 17 polypeptide 2/0.452
1evjNADGlucose--fructose oxidoreductase1.1.99.280.451
1g2vTTPGlucose-1-phosphate thymidylyltransferase/0.451
3n61H4BNitric oxide synthase, brain1.14.13.390.451
3x0c5GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.451
2zsaADPPantothenate kinase2.7.1.330.450
3ge6FMNNitroreductase/0.450
3jwvH4BNitric oxide synthase, brain1.14.13.390.450
3mp3HGGHydroxymethylglutaryl-CoA lyase, mitochondrial4.1.3.40.450
4cx3H4BNitric oxide synthase, brain1.14.13.390.450
4i1c1BEBeta-secretase 13.4.23.460.450
4lb9EVPSerum albumin/0.450
1jk3BATMacrophage metalloelastase3.4.24.650.449
3ojoPDCCap5O/0.449
4f5yC2EStimulator of interferon genes protein/0.449
5a65TPPThiamine-triphosphatase3.6.1.280.449
1dgbNDPCatalase1.11.1.60.448
2jb4A14Isopenicillin N synthase1.21.3.10.448
2zs8ADPPantothenate kinase2.7.1.330.448
1icvFMNOxygen-insensitive NAD(P)H nitroreductase/0.447
1oonFMNOxygen-insensitive NAD(P)H nitroreductase/0.447
2vbpVB1Isopenicillin N synthase1.21.3.10.447
3k5fAYHBeta-secretase 13.4.23.460.447
3od48XQHypoxia-inducible factor 1-alpha inhibitor1.14.11.300.447
3rqkH4BNitric oxide synthase, brain1.14.13.390.447
4fvzH4BNitric oxide synthase, brain1.14.13.390.447
1zw9H64ATP-dependent molecular chaperone HSP82/0.446
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
2getCOKPantothenate kinase2.7.1.330.446
2jnpNGHStromelysin-13.4.24.170.446
3nlwH4BNitric oxide synthase, brain1.14.13.390.446
3zoiM2WIsopenicillin N synthase1.21.3.10.446
4fvxH4BNitric oxide synthase, brain1.14.13.390.446
4fw0H4BNitric oxide synthase, brain1.14.13.390.446
4j7hTRHPCZA361.3/0.446
2fhlBNIAvidin-related protein 4/5/0.445
2vbdV10Isopenicillin N synthase1.21.3.10.445
2vprTDCTetracycline repressor protein class H/0.445
2x86ADPADP-L-glycero-D-manno-heptose-6-epimerase/0.445
3tlc7MDMicrocin C7 self-immunity protein MccF/0.445
3ufwH4BNitric oxide synthase, brain1.14.13.390.445
3zg6APRNAD-dependent protein deacetylase sirtuin-63.5.10.445
4ise1FWGlucokinase2.7.1.20.445
1w0kADPATP synthase subunit alpha, mitochondrial/0.444
1w0kADPATP synthase subunit beta, mitochondrial3.6.3.140.444
1yciNDFHypoxia-inducible factor 1-alpha inhibitor1.14.11.300.444
3gcq1BUMitogen-activated protein kinase 14/0.444
3ptzUDXUDP-glucose 6-dehydrogenase1.1.1.220.444
5a02NAPGlucose-fructose oxidoreductase/0.444
5a03NDPGlucose-fructose oxidoreductase/0.444
1ofgNDPGlucose--fructose oxidoreductase1.1.99.280.443
1qiqACCIsopenicillin N synthase1.21.3.10.443
1s64778Geranylgeranyl transferase type-1 subunit beta2.5.1.590.443
1tllFMNNitric oxide synthase, brain1.14.13.390.443
2xeiARKGlutamate carboxypeptidase 23.4.17.210.443
2y6fM9FIsopenicillin N synthase1.21.3.10.443
3c3xNAPEugenol synthase 11.1.1.3180.443
3ghh2NFCD38 molecule/0.443
4mv8ACPBiotin carboxylase6.3.4.140.443
2a0xDIHPurine nucleoside phosphorylase2.4.2.10.442
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.442
3abxRCBGlucanase/0.442
3aezGDPPantothenate kinase2.7.1.330.442
3hdqGDUUDP-galactopyranose mutase/0.442
3tleGSUMicrocin C7 self-immunity protein MccF/0.442
3ufqH4BNitric oxide synthase, brain1.14.13.390.442
1mmvH4BNitric oxide synthase, brain1.14.13.390.441
1rs6H4BNitric oxide synthase, brain1.14.13.390.441
2hizLIJBeta-secretase 13.4.23.460.441
3cluFADElectron transfer flavoprotein subunit alpha/0.441
3dhaC6LN-acyl homoserine lactonase AiiA3.1.1.810.441
3jt8H4BNitric oxide synthase, brain1.14.13.390.441
3jtaH4BNitric oxide synthase, brain1.14.13.390.441
3mz9BHNNickel-binding periplasmic protein/0.441
3nt2NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase1.1.1.180.441
3uftH4BNitric oxide synthase, brain1.14.13.390.441
4iix1EGMicrocin C7 self-immunity protein MccF/0.441
4l1fCOSAcyl-CoA dehydrogenase domain protein/0.441
5bv3M7Gm7GpppX diphosphatase3.6.1.590.441
5ig2NADShort-chain dehydrogenase/reductase SDR/0.441
1k2uH4BNitric oxide synthase, brain1.14.13.390.440
2pa3NAID-3-phosphoglycerate dehydrogenase1.1.1.950.440
2z9dFMNFMN-dependent NADH-azoreductase/0.440
2zseACPPantothenate kinase2.7.1.330.440
3fr5I4AFatty acid-binding protein, adipocyte/0.440
3pfhT3QdTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase2.1.1.2350.440
4jsgH4BNitric oxide synthase, brain1.14.13.390.440