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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
1rxjBNIStreptavidin

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
1rxjBNIStreptavidin/1.000
2c9zQUEAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.527
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.508
4gd9BTNStreptavidin/0.499
2c1zKMPAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.495
4ms1381Gamma-aminobutyric acid type B receptor subunit 1/0.495
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.494
3m2vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.492
2c1zU2FAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.485
2w6cBM4Acetylcholinesterase3.1.1.70.485
1swgBTNStreptavidin/0.482
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.482
4j7hTRHPCZA361.3/0.480
1kyvRBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.478
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.478
1xf0ASDAldo-keto reductase family 1 member C3/0.476
2xufTZ4Acetylcholinesterase3.1.1.70.476
2zevIPEGeranylgeranyl pyrophosphate synthase/0.475
4mr72BVGamma-aminobutyric acid type B receptor subunit 1/0.474
3r43ID8Aldo-keto reductase family 1 member C3/0.473
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.472
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.472
3uweVJJAldo-keto reductase family 1 member C3/0.472
3af1GDPPantothenate kinase2.7.1.330.470
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.470
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.469
2gbyBRNHTH-type transcriptional regulator QacR/0.469
3zj7C1KStrictosidine-O-beta-D-glucosidase3.2.1.1050.469
1oynROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.468
4i9z5BAcGMP-specific 3',5'-cyclic phosphodiesterase/0.468
1s2cFLFAldo-keto reductase family 1 member C3/0.467
4lm4JPZcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.466
1xonPILcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.465
1y2c3DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.465
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.465
3wd9QPCcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.465
1a26CNAPoly [ADP-ribose] polymerase 12.4.2.300.464
1lkeDOGBilin-binding protein/0.464
1ut6A8NAcetylcholinesterase3.1.1.70.464
3m30COMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.464
3m30COMMethyl-coenzyme M reductase I subunit beta2.8.4.10.464
1uhoVDNcGMP-specific 3',5'-cyclic phosphodiesterase/0.462
2xupTZ5Acetylcholinesterase3.1.1.70.462
3d3p20AcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.462
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
4fcb0T7cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.462
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.461
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.461
4gutFADLysine-specific histone demethylase 1B10.461
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.460
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.460
4ajdF04cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.460
1g63FMNEpidermin decarboxylase4.1.10.459
1lnmDTXBilin-binding protein/0.459
1ro98BRcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.459
1sd2MTHS-methyl-5'-thioadenosine phosphorylase/0.459
1u65CP0Acetylcholinesterase3.1.1.70.459
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.459
3fsjD7KBenzoylformate decarboxylase4.1.1.70.459
1nquRDL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.458
1zgcA2EAcetylcholinesterase3.1.1.70.458
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.458
3k4s0MOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.458
3zv7NHGAcetylcholinesterase3.1.1.70.458
1zgbA1EAcetylcholinesterase3.1.1.70.457
3djlFADPutative acyl-CoA dehydrogenase AidB1.3.990.457
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.457
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.457
3v94WYQPhosphodiesterase/0.457
5dp2NAPCurF/0.457
3emlZMAAdenosine receptor A2a/0.457
2geuCOKPantothenate kinase2.7.1.330.456
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.456
4b66NAPL-ornithine N(5)-monooxygenase/0.456
4fcd0T6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.456
4g2wNI0cGMP-specific 3',5'-cyclic phosphodiesterase/0.456
1dhfFOLDihydrofolate reductase1.5.1.30.455
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.455
3c1oNAPEugenol synthase/0.455
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
3rgzBLDProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.455
4ajgF07cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.455
4dbw511Aldo-keto reductase family 1 member C3/0.455
4hf415HcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.455
4llkMEWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.455
1zuaTOLAldo-keto reductase family 1 member B101.1.10.454
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.454
2vbpVB1Isopenicillin N synthase1.21.3.10.454
2xuiTZ5Acetylcholinesterase3.1.1.70.454
3q2jCKIAminoglycoside 3'-phosphotransferase2.7.1.950.454
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.454
1dx6GNTAcetylcholinesterase3.1.1.70.453
1e66HUXAcetylcholinesterase3.1.1.70.453
1h60STRPentaerythritol tetranitrate reductase/0.453
3aezGDPPantothenate kinase2.7.1.330.453
3zkuHCVIsopenicillin N synthase1.21.3.10.453
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
5a0yCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.453
5a0yCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.453
1b2lNDCAlcohol dehydrogenase1.1.1.10.452
1so2666cGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.452
1v3q2DIPurine nucleoside phosphorylase2.4.2.10.452
2ckmAA7Acetylcholinesterase3.1.1.70.452
3af2ACPPantothenate kinase2.7.1.330.452
3uzxAOX3-oxo-5-beta-steroid 4-dehydrogenase/0.452
4usqFADPyridine nucleotide-disulfide oxidoreductase/0.452
4x9dU5PUncharacterized protein MJ1435/0.452
1zq5E04Aldo-keto reductase family 1 member C3/0.451
4ajm3A6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.451
4fhd0TTSpore photoproduct lyase/0.451
4lcw1VYMajor histocompatibility complex class I-related gene protein/0.451
1efyBZCPoly [ADP-ribose] polymerase 12.4.2.300.450
1p5rCOAFormyl-CoA:oxalate CoA-transferase/0.450
3af3GCPPantothenate kinase2.7.1.330.450
1w87FADFerredoxin--NADP reductase1.18.1.20.449
2o8h227cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.449
3aosJH2Hemolymph juvenile hormone binding protein/0.449
3casASD3-oxo-5-beta-steroid 4-dehydrogenase/0.449
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
4b4w9L9Bifunctional protein FolD/0.449
1h36R88Squalene--hopene cyclase4.2.1.1290.448
3aivHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic3.2.1.1820.448
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
4bfsZVSPantothenate kinase2.7.1.330.448
1dghNDPCatalase1.11.1.60.447
1odcA8BAcetylcholinesterase3.1.1.70.447
1paxDHQPoly [ADP-ribose] polymerase 12.4.2.300.447
2f3815MAldo-keto reductase family 1 member C3/0.447
2hxzH7JCathepsin S3.4.22.270.447
2xviFADPutative flavin-containing monooxygenase/0.447
3m2uCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.447
3wavDWVEctonucleotide pyrophosphatase/phosphodiesterase family member 23.1.4.390.447
4ey6GNTAcetylcholinesterase3.1.1.70.447
1eveE20Acetylcholinesterase3.1.1.70.446
2b8jADNClass B acid phosphatase3.1.3.20.446
2ipjFFAAldo-keto reductase family 1 member C2/0.446
2ovvPFHcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.446
2weyEV1cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.446
2z52H23Geranylgeranyl pyrophosphate synthase/0.446
3nu03TUDihydrofolate reductase1.5.1.30.446
3rtnRTNBeta-secretase 13.4.23.460.446
4ey7E20Acetylcholinesterase3.1.1.70.446
1q5mNDPProstaglandin-E(2) 9-reductase1.1.1.1890.445
1udtVIAcGMP-specific 3',5'-cyclic phosphodiesterase/0.445
1x8b824Wee1-like protein kinase2.7.10.20.445
1y2e5DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.445
2bu9HFVIsopenicillin N synthase1.21.3.10.445
2poqISDTrans-1,2-dihydrobenzene-1,2-diol dehydrogenase1.3.1.200.445
3ha5SFGHydroxymycolate synthase MmaA42.1.10.445
3hl0NADMaleylacetate reductase/0.445
3v0p4GWHisto-blood group ABO system transferase/0.445
4b4vL34Bifunctional protein FolD/0.445
4nv14TGFormyl transferase/0.445
1u0wSTLChalcone synthase 22.3.1.740.444
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.444
2cmfF11Acetylcholinesterase3.1.1.70.444
2uxoTACHTH-type transcriptional regulator TtgR/0.444
2xuoTZ4Acetylcholinesterase3.1.1.70.444
3e6eDCSAlanine racemase/0.444
3zkyWT4Isopenicillin N synthase1.21.3.10.444
4ajfF03cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
5a4wQCTGlutathione S-transferase F22.5.1.180.444
5cxv0HKMuscarinic acetylcholine receptor M1/0.444
1ni4TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.443
1ni4TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.443
1y2d4DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
2ouyCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
3eon341Glutaryl-CoA dehydrogenase/0.443
3hbfMYCFlavonoid 3-O-glucosyltransferase2.4.10.443
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
3ug8IMNAldo-keto reductase family 1 member C3/0.443
4ddl0JQcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
4dpdDHFBifunctional dihydrofolate reductase-thymidylate synthase/0.443
4js1CTNBeta-galactoside alpha-2,6-sialyltransferase 12.4.99.10.443
4ts7ADPPurine phosphoribosyltransferase (GpT-1)/0.443
1p0pBCHCholinesterase3.1.1.80.442
1s20NAD2,3-diketo-L-gulonate reductase1.1.1.1300.442
1zdwFLVPrenyltransferase/0.442
2aouCQAHistamine N-methyltransferase2.1.1.80.442
2b82ADNClass B acid phosphatase3.1.3.20.442
2in6839Wee1-like protein kinase2.7.10.20.442
2j3qTFLAcetylcholinesterase3.1.1.70.442
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3fznD7KBenzoylformate decarboxylase4.1.1.70.442
3h3r14HCollagen type IV alpha-3-binding protein/0.442
4epq0RRPoly(ADP-ribose) glycohydrolase/0.442
1o5gCR9Prothrombin3.4.21.50.441
1rkwPNTHTH-type transcriptional regulator QacR/0.441
1sd1FMCS-methyl-5'-thioadenosine phosphorylase/0.441
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.441
2qw8NAPEugenol synthase 11.1.1.3180.441
2xuhTZ4Acetylcholinesterase3.1.1.70.441
3gn73GNPoly [ADP-ribose] polymerase 12.4.2.300.441
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.441
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.441
1fmlRTLRetinol dehydratase/0.440
1obnASVIsopenicillin N synthase1.21.3.10.440
1wm1PTBProline iminopeptidase3.4.11.50.440
1x1aSAMC-20 methyltransferase/0.440
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2fm0M98cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2vcmM11Isopenicillin N synthase1.21.3.10.440
2y60M8FIsopenicillin N synthase1.21.3.10.440
3fr5I4AFatty acid-binding protein, adipocyte/0.440
3iakEV1cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
4b67NAPL-ornithine N(5)-monooxygenase/0.440
4boeCLRJapanin/0.440
4e0u0MVCyclic dipeptide N-prenyltransferase/0.440
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.440
4gv7MEWPoly [ADP-ribose] polymerase 12.4.2.300.440
4relKMPGlycosyltransferase/0.440
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.440