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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
4nxv GDP Mitochondrial dynamics protein MID51

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4nxv GDPMitochondrial dynamics protein MID51 / 0.843
4nxx GDPMitochondrial dynamics protein MID51 / 0.711
4oag ADPMitochondrial dynamics protein MID51 / 0.690
3bt9 DEQHTH-type transcriptional regulator QacR / 0.662
1bcu PRLProthrombin 3.4.21.5 0.660
1c4y IH3Prothrombin 3.4.21.5 0.660
1cqs EQUSteroid Delta-isomerase 5.3.3.1 0.660
1crb RTLRetinol-binding protein 1 / 0.660
1cx2 S58Prostaglandin G/H synthase 2 1.14.99.1 0.660
1d3d BZTProthrombin 3.4.21.5 0.660
1e7a PFLSerum albumin / 0.660
1ezv SMACytochrome b / 0.660
1f0q EMOCasein kinase II subunit alpha 2.7.11.1 0.660
1fdu ESTEstradiol 17-beta-dehydrogenase 1 1.1.1.62 0.660
1g9c BABBotulinum neurotoxin type B 3.4.24.69 0.660
1hk5 T44Serum albumin / 0.660
1hnv TBOGag-Pol polyprotein 2.7.7.49 0.660
1hqu HBYGag-Pol polyprotein 2.7.7.49 0.660
1i05 LTLMajor urinary protein 6 / 0.660
1i9m INWCarbonic anhydrase 2 4.2.1.1 0.660
1ikv EFZGag-Pol polyprotein 2.7.7.49 0.660
1iky MSDGag-Pol polyprotein 2.7.7.49 0.660
1irj CPSProtein S100-A9 / 0.660
1jla TNKGag-Pol polyprotein 2.7.7.49 0.660
1jlg UC1Gag-Pol polyprotein 2.7.7.49 0.660
1jlq SBNGag-Pol polyprotein 2.7.7.49 0.660
1jut LYDThymidylate synthase / 0.660
1jx0 DFVChalcone--flavonone isomerase 1 5.5.1.6 0.660
1kb9 SMACytochrome b / 0.660
1kgj FL8Transthyretin / 0.660
1kqw RTLCellular retinol-binding protein type II / 0.660
1kzu RG1Light-harvesting protein B-800/850 alpha chain / 0.660
1kzu RG1Light-harvesting protein B-800/850 beta chain / 0.660
1m9t INENitric oxide synthase, inducible 1.14.13.39 0.660
1n83 CLRNuclear receptor ROR-alpha / 0.660
1o6q R17Squalene--hopene cyclase 4.2.1.129 0.660
1odc A8BAcetylcholinesterase 3.1.1.7 0.660
1pj6 FOLDimethylglycine oxidase 1.5.3.10 0.660
1pq9 44BOxysterols receptor LXR-beta / 0.660
1pqc 444Oxysterols receptor LXR-beta / 0.660
1q20 PLOSulfotransferase family cytosolic 2B member 1 2.8.2.2 0.660
1qiw DPDCalmodulin / 0.660
1qjg EQUSteroid Delta-isomerase 5.3.3.1 0.660
1qti GNTAcetylcholinesterase 3.1.1.7 0.660
1qvt PRLHTH-type transcriptional regulator QacR / 0.660
1rev TB9Gag-Pol polyprotein 2.7.7.49 0.660
1rpw DIDHTH-type transcriptional regulator QacR / 0.660
1rt2 TNKGag-Pol polyprotein 2.7.7.49 0.660
1rt5 UC2Gag-Pol polyprotein 2.7.7.49 0.660
1rti HEFGag-Pol polyprotein 2.7.7.49 0.660
1s1v TNKGag-Pol polyprotein 2.7.7.49 0.660
1sej F89Bifunctional dihydrofolate reductase-thymidylate synthase / 0.660
1suo CPZCytochrome P450 2B4 1.14.14.1 0.660
1tkx GWBGag-Pol polyprotein 2.7.7.49 0.660
1tkz H16Gag-Pol polyprotein 2.7.7.49 0.660
1tl3 H20Gag-Pol polyprotein 2.7.7.49 0.660
1tvr TB9Gag-Pol polyprotein 2.7.7.49 0.660
1u0w STLChalcone synthase 2 2.3.1.74 0.660
1u65 CP0Acetylcholinesterase 3.1.1.7 0.660
1uym PU3Heat shock protein HSP 90-beta / 0.660
1vru AAPGag-Pol polyprotein 2.7.7.49 0.660
1vzd CB3Thymidylate synthase / 0.660
1w4l GL8Acetylcholinesterase 3.1.1.7 0.660
1w6j R71Lanosterol synthase 5.4.99.7 0.660
1w76 GNTAcetylcholinesterase 3.1.1.7 0.660
1wxy FRKAdenosine deaminase 3.5.4.4 0.660
1ysw 43BApoptosis regulator Bcl-2 / 0.660
1z1f STLResveratrol synthase / 0.660
1zg3 2HIIsoflavone 4'-O-methyltransferase / 0.660
1zga HMKIsoflavone 4'-O-methyltransferase / 0.660
1zhw HC2Oxysterol-binding protein homolog 4 / 0.660
1zhy CLROxysterol-binding protein homolog 4 / 0.660
1zhz ERGOxysterol-binding protein homolog 4 / 0.660
1zz1 SHHHistone deacetylase-like amidohydrolase 3.5.1 0.660
2a8g GNGAvidin / 0.660
2acl L05Oxysterols receptor LXR-alpha / 0.660
2agv BHQSarcoplasmic/endoplasmic reticulum calcium ATPase 1 3.6.3.8 0.660
2aot 2PMHistamine N-methyltransferase 2.1.1.8 0.660
2aov C2MHistamine N-methyltransferase 2.1.1.8 0.660
2azy CHDPhospholipase A2, major isoenzyme 3.1.1.4 0.660
2b5j 3ACGag-Pol polyprotein 2.7.7.49 0.660
2ban 357Gag-Pol polyprotein 2.7.7.49 0.660
2bjf DXCCholoylglycine hydrolase 3.5.1.24 0.660
2cgf P2NATP-dependent molecular chaperone HSP82 / 0.660
2ci0 1CMLanosterol 14-alpha demethylase 1.14.13.70 0.660
2ckm AA7Acetylcholinesterase 3.1.1.7 0.660
2eau CZASarcoplasmic/endoplasmic reticulum calcium ATPase 1 3.6.3.8 0.660
2fhj H4ZFormylmethanofuran--tetrahydromethanopterin formyltransferase 2.3.1.101 0.660
2fyp RDEEndoplasmin / 0.660
2g44 T3OEstrogen receptor / 0.660
2gby BRNHTH-type transcriptional regulator QacR / 0.660
2giu FBREstrogen receptor beta / 0.660
2gm1 2AZKinesin-like protein KIF11 / 0.660
2gyw OBIAcetylcholinesterase 3.1.1.7 0.660
2hnz PC0Gag-Pol polyprotein 2.7.7.49 0.660
2hz4 4STTyrosine-protein kinase ABL1 2.7.10.2 0.660
2ic3 HBYGag-Pol polyprotein 2.7.7.49 0.660
2j0k 4STFocal adhesion kinase 1 2.7.10.2 0.660
2j2i LY4Serine/threonine-protein kinase pim-1 2.7.11.1 0.660
2kb2 FMNUncharacterized protein / 0.660
2kot ANWProtein S100-A13 / 0.660
2o21 43BApoptosis regulator Bcl-2 / 0.660
2ocf ESTEstrogen receptor / 0.660
2ohv NHLGlutamate racemase / 0.660
2opb F21Phenylethanolamine N-methyltransferase 2.1.1.28 0.660
2pvh P19Casein kinase II subunit alpha 2.7.11.1 0.660
2q5y TYR_GLY_LEUNuclear pore complex protein Nup98-Nup96 / 0.660
2q6h CXXNa(+):neurotransmitter symporter (Snf family) / 0.660
2qei CXXNa(+):neurotransmitter symporter (Snf family) / 0.660
2r9k SGIBeta-galactoside-specific lectin 1 / 0.660
2rbe ZMGCorticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.660
2std CRPScytalone dehydratase 4.2.1.94 0.660
2uxp CLMHTH-type transcriptional regulator TtgR / 0.660
2v61 C18Amine oxidase [flavin-containing] B 1.4.3.4 0.660
2vg5 NNCGag-Pol polyprotein 2.7.7.49 0.660
2vg7 NNIGag-Pol polyprotein 2.7.7.49 0.660
2vuk P83Cellular tumor antigen p53 / 0.660
2w0b CMWLanosterol 14-alpha demethylase 1.14.13.70 0.660
2w4i VGAGlutamate racemase / 0.660
2whq HI6Acetylcholinesterase 3.1.1.7 0.660
2xby 63CCoagulation factor X 3.4.21.6 0.660
2xc5 OYJCoagulation factor X 3.4.21.6 0.660
2xnv VU3Soluble acetylcholine receptor / 0.660
2xuf TZ4Acetylcholinesterase 3.1.1.7 0.660
2xuk TZ5Acetylcholinesterase 3.1.1.7 0.660
2xw1 9NVSerum albumin / 0.660
2xys SY9Soluble acetylcholine receptor / 0.660
2ycs NXPSerine/threonine-protein kinase Chk2 2.7.11.1 0.660
2yne YNEGlycylpeptide N-tetradecanoyltransferase / 0.660
2zdx P4A[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial 2.7.11.2 0.660
3acw 651Dehydrosqualene synthase / 0.660
3ar4 TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 3.6.3.8 0.660
3arq DM5Chitinase A / 0.660
3ayg HQONitric oxide reductase / 0.660
3bi4 298Polyamine oxidase FMS1 / 0.660
3bpt QUE3-hydroxyisobutyryl-CoA hydrolase, mitochondrial 3.1.2.4 0.660
3c4e C4ESerine/threonine-protein kinase pim-1 2.7.11.1 0.660
3cgy RDCVirulence sensor histidine kinase PhoQ 2.7.13.3 0.660
3clx X22E3 ubiquitin-protein ligase XIAP 6.3.2 0.660
3d27 W29Methionine aminopeptidase / 0.660
3d73 NBBPheromone-binding protein ASP1 / 0.660
3d74 NBBPheromone-binding protein ASP1 / 0.660
3dl9 V2HVitamin D 25-hydroxylase / 0.660
3dnd LL2cAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.660
3dy8 IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A / 0.660
3dyq IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A / 0.660
3ej0 11XInorganic pyrophosphatase / 0.660
3ey4 352Corticosteroid 11-beta-dehydrogenase isozyme 1 1.1.1.146 0.660
3f3y 4OABile salt sulfotransferase 2.8.2.14 0.660
3foo PXXSoluble cytochrome b562 / 0.660
3gcm 5GPPolyribonucleotide nucleotidyltransferase / 0.660
3ggs 2FDPurine nucleoside phosphorylase 2.4.2.1 0.660
3gw9 VNILanosterol 14-alpha-demethylase / 0.660
3gwu SRENa(+):neurotransmitter symporter (Snf family) / 0.660
3hxe BD8Geranylgeranyl transferase type-2 subunit beta 2.5.1.60 0.660
3i64 DNA2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.660
3inj BXBAldehyde dehydrogenase, mitochondrial 1.2.1.3 0.660
3inl BXBAldehyde dehydrogenase, mitochondrial 1.2.1.3 0.660
3ipt EQUSteroid Delta-isomerase 5.3.3.1 0.660
3iu9 T07Methionine aminopeptidase 2 / 0.660
3iw8 HIZMitogen-activated protein kinase 14 / 0.660
3jx3 JI5Nitric oxide synthase, brain 1.14.13.39 0.660
3jx6 JI5Nitric oxide synthase, brain 1.14.13.39 0.660
3keg MREFMN-dependent NADH-azoreductase 1 / 0.660
3kyt HC2Nuclear receptor ROR-gamma / 0.660
3lal KRVGag-Pol polyprotein 2.7.7.49 0.660
3lam KRPGag-Pol polyprotein 2.7.7.49 0.660
3lw0 CCXInsulin-like growth factor 1 receptor 2.7.10.1 0.660
3lzz GDPUncharacterized protein / 0.660
3m6g LO3Actin, alpha skeletal muscle / 0.660
3m8p 65BGag-Pol polyprotein 2.7.7.49 0.660
3mdm FJZCholesterol 24-hydroxylase / 0.660
3mj5 GRMReplicase polyprotein 1a 3.4.22 0.660
3mpe N2ACathepsin S 3.4.22.27 0.660
3my5 RFZCyclin-dependent kinase 2 2.7.11.22 0.660
3myu VIBHigh affinity transport system protein p37 / 0.660
3neg PYVAbscisic acid receptor PYL1 / 0.660
3njo P2MAbscisic acid receptor PYR1 / 0.660
3nlj JRRNitric oxide synthase, brain 1.14.13.39 0.660
3nly 3XCNitric oxide synthase, brain 1.14.13.39 0.660
3nny 59RNitric oxide synthase, brain 1.14.13.39 0.660
3nzk C90UDP-3-O-acyl-N-acetylglucosamine deacetylase / 0.660
3o73 O73Ribosyldihydronicotinamide dehydrogenase [quinone] / 0.660
3oht 1N1Mitogen-activated protein kinase / 0.660
3oq6 PFBAlcohol dehydrogenase E chain 1.1.1.1 0.660
3owy EQUSteroid Delta-isomerase 5.3.3.1 0.660
3p99 LNPLanosterol 14-alpha-demethylase / 0.660
3pah XDEPhenylalanine-4-hydroxylase 1.14.16.1 0.660
3pm1 ETHTH-type transcriptional regulator QacR / 0.660
3pmu F7LEndothiapepsin 3.4.23.22 0.660
3q92 XNBKetohexokinase / 0.660
3qgd 26SGenome polyprotein 2.7.7.48 0.660
3qgf 46FGenome polyprotein 2.7.7.48 0.660
3qi4 IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A / 0.660
3qm4 PN0Cytochrome P450 2D6 / 0.660
3rox TEPNAD(P)H-hydrate epimerase 5.1.99.6 0.660
3ruk AERSteroid 17-alpha-hydroxylase/17,20 lyase / 0.660
3s1c ZIRCytokinin dehydrogenase 1 1.5.99.12 0.660
3s7b NH5N-lysine methyltransferase SMYD2 / 0.660
3sff 0DIHistone deacetylase 8 3.5.1.98 0.660
3sfh 1DIHistone deacetylase 8 3.5.1.98 0.660
3svq JK4Nitric oxide synthase, brain 1.14.13.39 0.660
3szf DCQSulfide-quinone reductase / 0.660
3t11 3T1Gag-Pol polyprotein 3.4.23.16 0.660
3tda PN0Cytochrome P450 2D6 / 0.660
3tdj 3TJGlutamate receptor 2 / 0.660
3tk3 CPZCytochrome P450 2B4 1.14.14.1 0.660
3u3o 3QVSulfotransferase 1A1 2.8.2.1 0.660
3u78 E67Lysine-specific demethylase 7A 1.14.11 0.660
3u9n 09HSerine/threonine-protein kinase Chk1 2.7.11.1 0.660
3ufs HW6Nitric oxide synthase, brain 1.14.13.39 0.660
3uft HW7Nitric oxide synthase, brain 1.14.13.39 0.660
3v1s 0LHStrictosidine synthase 4.3.3.2 0.660
3vev 0H4Glucokinase 2.7.1.2 0.660
3wsb RWZFarnesyltransferase, putative / 0.660
3zr7 OR8Progesterone receptor / 0.660
3zra ORBProgesterone receptor / 0.660
3zrb ORCProgesterone receptor / 0.660
4a5y G7XKinesin-like protein KIF11 / 0.660
4a9r RU5Serine/threonine-protein kinase Chk2 2.7.11.1 0.660
4b71 DJLGenome polyprotein 3.4.21.98 0.660
4b76 PW1Genome polyprotein 3.4.21.98 0.660
4b7z Q4QAcetylcholinesterase 3.1.1.7 0.660
4b8u IBK3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase 4.2.1.59 0.660
4bbh YBNGlycylpeptide N-tetradecanoyltransferase / 0.660
4bqg 50QHeat shock protein HSP 90-alpha / 0.660
4chy C5QIntegrase / 0.660
4cx3 HW8Nitric oxide synthase, brain 1.14.13.39 0.660
4dij BLFE3 ubiquitin-protein ligase Mdm2 6.3.2 0.660
4dkv 0KWEnvelope glycoprotein gp160 / 0.660
4dlj 6RGMitogen-activated protein kinase 14 / 0.660
4dvq 1CACytochrome P450 11B2, mitochondrial 1.14.15.4 0.660
4dwv PFBAlcohol dehydrogenase E chain 1.1.1.1 0.660
4e0u 0MVCyclic dipeptide N-prenyltransferase / 0.660
4e6a 0O9Mitogen-activated protein kinase 14 / 0.660
4e70 N7IConiferyl alcohol 9-O-methyltransferase / 0.660
4ea0 651Dehydrosqualene synthase / 0.660
4eft EFTHeat shock protein HSP 90-alpha / 0.660
4eh6 IRGMitogen-activated protein kinase 14 / 0.660
4eh7 0OOMitogen-activated protein kinase 14 / 0.660
4ejv LCLTranscriptional regulator TcaR / 0.660
4erw STUCyclin-dependent kinase 2 2.7.11.22 0.660
4fxy 0W2Neurolysin, mitochondrial 3.4.24.16 0.660
4g09 0VDHistidinol dehydrogenase / 0.660
4g3j VNTLanosterol 14-alpha-demethylase / 0.660
4g48 PZBMycocyclosin synthase 1.14.21.9 0.660
4g7g VFVLanosterol 14-alpha-demethylase / 0.660
4guk P2GNeuronal calcium sensor 1 / 0.660
4hdr DMDNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase / 0.660
4hdr DMDArsB / 0.660
4hfn CIY2-alkenal reductase (NADP(+)-dependent) / 0.660
4hmb PZZPhospholipase A2 VRV-PL-VIIIa / 0.660
4hz5 19YDNA topoisomerase 4 subunit B / 0.660
4i1r LZUMucosa-associated lymphoid tissue lymphoma translocation protein 1 3.4.22 0.660
4ig0 1FGGag-Pol polyprotein 2.7.7.49 0.660
4iyg 1HUStrictosidine synthase 4.3.3.2 0.660
4j6d TESCytochrome P450 monooxygenase / 0.660
4j7d I31E3 ubiquitin-protein ligase Mdm2 6.3.2 0.660
4jlj 1NMDeoxycytidine kinase 2.7.1.74 0.660
4jlk 1NODeoxycytidine kinase 2.7.1.74 0.660
4jlt 8PRCytochrome P450 2B4 1.14.14.1 0.660
4k3n 1OTM17 leucyl aminopeptidase / 0.660
4kfo 1QSNicotinamide phosphoribosyltransferase 2.4.2.12 0.660
4kqg DMDNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase 2.4.2.21 0.660
4lg5 A1OAbscisic acid receptor PYL2 / 0.660
4lm4 JPZcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A 3.1.4.17 0.660
4lmu QUESerine/threonine-protein kinase pim-1 2.7.11.1 0.660
4m0f 1YKAcetylcholinesterase 3.1.1.7 0.660
4m48 21BSodium-dependent dopamine transporter / 0.660
4man 1Y1Apoptosis regulator Bcl-2 / 0.660
4mme 29QNa(+):neurotransmitter symporter (Snf family) / 0.660
4n6h EJ4Delta-type opioid receptor / 0.660
4nbb 9CATerminal oxygenase component of carbazole / 0.660
4nbh 9CATerminal oxygenase component of carbazole / 0.660
4ng5 PFBAlcohol dehydrogenase E chain 1.1.1.1 0.660
4nkv AERSteroid 17-alpha-hydroxylase/17,20 lyase / 0.660
4o78 SAVBromodomain-containing protein 4 / 0.660
4ple CPSNuclear receptor subfamily 5 group A member 2 / 0.660
4qem HC4Phospholipase A2 VRV-PL-VIIIa / 0.660
4qer STLPhospholipase A2 VRV-PL-VIIIa / 0.660
4qjq OTRLactoperoxidase / 0.660
4r20 AERCytochrome P450 family 17 polypeptide 2 / 0.660
4rgs V55Repressor protein / 0.660
4ryv ZEAProtein LlR18A / 0.660
4tuv CPZCytochrome P450 119 1.14 0.660
4u95 MIYMultidrug efflux pump subunit AcrB / 0.660
4uym VOR14-alpha sterol demethylase Cyp51B / 0.660
4xoq F42Coenzyme F420:L-glutamate ligase / 0.660
4xp4 COCSodium-dependent dopamine transporter / 0.660
5a4w QCTGlutathione S-transferase F2 2.5.1.18 0.660
5alu HD2Bifunctional epoxide hydrolase 2 3.1.3.76 0.660
5c8a 5ADProbable transcriptional regulator / 0.660
5cdg PFBAlcohol dehydrogenase E chain 1.1.1.1 0.660
5cdt PFBAlcohol dehydrogenase E chain 1.1.1.1 0.660
5fli QUEQuercetinase QueD / 0.660
5kj1 PFBAlcohol dehydrogenase E chain 1.1.1.1 0.660
5kj6 PFBAlcohol dehydrogenase E chain 1.1.1.1 0.660
5kjc PFBAlcohol dehydrogenase E chain 1.1.1.1 0.660
7std CRPScytalone dehydratase 4.2.1.94 0.660
5xra CLRCannabinoid receptor 1 / 0.660
5l7d CLRSmoothened homolog / 0.660
5dhh DGWNociceptin receptor / 0.660
5dhg DGVNociceptin receptor / 0.660
4ej4 EJ4Delta-type opioid receptor / 0.660
3pbl ETQD(3) dopamine receptor / 0.660
3btj DEQHTH-type transcriptional regulator QacR / 0.659
1yho TRRDihydrofolate reductase 1.5.1.3 0.654
4nxw ADPMitochondrial dynamics protein MID51 / 0.654
1jt6 DEQHTH-type transcriptional regulator QacR / 0.652
2q66 ATPPoly(A) polymerase 2.7.7.19 0.652
1h46 RNPGlucanase / 0.650
3ken ZZDKinesin-like protein KIF11 / 0.650