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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
1drt PCV Clavaminate synthase 1 1.14.11.21

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1drt PCVClavaminate synthase 1 1.14.11.21 0.760
1eyn 2ANUDP-N-acetylglucosamine 1-carboxyvinyltransferase / 0.744
1gy3 ATPCyclin-dependent kinase 2 2.7.11.22 0.744
1h35 R01Squalene--hopene cyclase 4.2.1.129 0.744
1h36 R88Squalene--hopene cyclase 4.2.1.129 0.744
1kzj CB3Thymidylate synthase / 0.744
1o6q R17Squalene--hopene cyclase 4.2.1.129 0.744
1o6r R19Squalene--hopene cyclase 4.2.1.129 0.744
1p0p BCHCholinesterase 3.1.1.8 0.744
1qvn FRIInterleukin-2 / 0.744
1qw5 14WNitric oxide synthase, inducible 1.14.13.39 0.744
1vrq FONSubunit alpha of sarocosine oxidase / 0.744
1wrl TFPTroponin C, slow skeletal and cardiac muscles / 0.744
1xrp PRO_LEU_GLY_GLYProline iminopeptidase 3.4.11.5 0.744
1zzr DP9Nitric oxide synthase, brain 1.14.13.39 0.744
2c7x NRBCytochrome P450 monooxygenase PikC / 0.744
2ccu 2D9Heat shock protein HSP 90-alpha / 0.744
2g1q N9HKinesin-like protein KIF11 / 0.744
2gby BRNHTH-type transcriptional regulator QacR / 0.744
2j0k 4STFocal adhesion kinase 1 2.7.10.2 0.744
2q6h CXXNa(+):neurotransmitter symporter (Snf family) / 0.744
2tsc CB3Thymidylate synthase / 0.744
2wog ZZDKinesin-like protein KIF11 / 0.744
2xae 2XAKinesin-like protein KIF11 / 0.744
2xf3 J01Uncharacterized protein / 0.744
2xvv 9DNSerum albumin / 0.744
3b3p JI7Nitric oxide synthase, brain 1.14.13.39 0.744
3bhy 7CPDeath-associated protein kinase 3 / 0.744
3bug AEHBeta-secretase 1 3.4.23.46 0.744
3cy2 MB9Serine/threonine-protein kinase pim-1 2.7.11.1 0.744
3cz0 9ODPheromone-binding protein ASP1 / 0.744
3el5 1UNGag-Pol polyprotein / 0.744
3fo7 IMNPhospholipase A2 VRV-PL-VIIIa / 0.744
3hii PNTAmiloride-sensitive amine oxidase [copper-containing] / 0.744
3jws JI4Nitric oxide synthase, brain 1.14.13.39 0.744
3jx0 JI4Nitric oxide synthase, brain 1.14.13.39 0.744
3ken ZZDKinesin-like protein KIF11 / 0.744
3mj5 GRMReplicase polyprotein 1a 3.4.22 0.744
3nc9 TR3Ketohexokinase / 0.744
3nfa CBJGag-Pol polyprotein / 0.744
3ngq 1PSCCR4-NOT transcription complex subunit 6-like 3.1.13.4 0.744
3nks ACJProtoporphyrinogen oxidase 1.3.3.4 0.744
3nln JRSNitric oxide synthase, brain 1.14.13.39 0.744
3nlv 3XANitric oxide synthase, brain 1.14.13.39 0.744
3qa2 XNAKetohexokinase / 0.744
3tmz 06XCytochrome P450 2B4 1.14.14.1 0.744
3tym 08RNitric oxide synthase, brain 1.14.13.39 0.744
3ufo HW4Nitric oxide synthase, brain 1.14.13.39 0.744
3ufr H5WNitric oxide synthase, brain 1.14.13.39 0.744
3wsb RWZFarnesyltransferase, putative / 0.744
4awg CI3Polymerase acidic protein / 0.744
4b6u M7GEukaryotic translation initiation factor 4E type 3 / 0.744
4b76 PW1Genome polyprotein 3.4.21.98 0.744
4bbg V02Kinesin-like protein KIF11 / 0.744
4c1f X8ZMetallo-beta-lactamase type 2 / 0.744
4ea1 3RXDehydrosqualene synthase / 0.744
4eil CB3Bifunctional dihydrofolate reductase-thymidylate synthase 1.5.1.3 0.744
4iqq D16Thymidylate synthase / 0.744
4jhz 1KVBeta-glucuronidase 3.2.1.31 0.744
4kla CHDFerrochelatase, mitochondrial 4.99.1.1 0.744
4mm9 FVXNa(+):neurotransmitter symporter (Snf family) / 0.744
5bmv VLBTubulin alpha-1B chain / 0.744
5bmv VLBTubulin beta chain / 0.744
5dby DIFSerum albumin / 0.744
5jqb IBPEnvelope glycoprotein / 0.744
5k0t 415Methionine--tRNA ligase / 0.744
3wiy LC6Induced myeloid leukemia cell differentiation protein Mcl-1 / 0.690
4j16 NADNAD/NADP transhydrogenase alpha subunit 1 / 0.690
2l1r SXKTroponin C, slow skeletal and cardiac muscles / 0.689
3bej MUFBile acid receptor / 0.688
3gnc QQQGlutaryl-CoA dehydrogenase / 0.688
2r0g 7CKPutative FAD-monooxygenase / 0.686
2vd0 D27Hematopoietic prostaglandin D synthase / 0.683
4bae RWXDNA gyrase subunit B / 0.683
4e5j 581Polymerase acidic protein / 0.681
13gs SASGlutathione S-transferase P 2.5.1.18 0.680
3lfc Z86Mitogen-activated protein kinase 14 / 0.680
4z9r NADOmega-3 polyunsaturated fatty acid synthase subunit PfaD / 0.679
2y00 Y01Beta-1 adrenergic receptor / 0.678
1rb3 MTXDihydrofolate reductase 1.5.1.3 0.676
3c6n 2S8Protein TRANSPORT INHIBITOR RESPONSE 1 / 0.675
1u5c BIKL-lactate dehydrogenase 1.1.1.27 0.670
3gfb NADL-threonine 3-dehydrogenase / 0.668
2qc8 ADPGlutamine synthetase 6.3.1.2 0.666
2ch2 KY1Serine--pyruvate aminotransferase / 0.665
2d3a ADPGlutamine synthetase root isozyme 3 6.3.1.2 0.664
1rc4 DDFDihydrofolate reductase 1.5.1.3 0.663
3mw0 BHRNickel-binding periplasmic protein / 0.663
4ej1 FOLDihydrofolate reductase 1.5.1.3 0.663
1dyi FOLDihydrofolate reductase 1.5.1.3 0.662
1mdl RMNMandelate racemase / 0.662
1qmf KEFPenicillin-binding protein 2x / 0.662
2i4m PSDProline--tRNA ligase 6.1.1.15 0.662
4i9u 1E7L-lactate dehydrogenase A chain 1.1.1.27 0.662
4ph9 IBPProstaglandin G/H synthase 2 1.14.99.1 0.661
1c5n ESIProthrombin 3.4.21.5 0.660
1d4p BPPProthrombin 3.4.21.5 0.660
1juj LYAThymidylate synthase 2.1.1.45 0.660
1o2g 696Prothrombin 3.4.21.5 0.660
1owi 426Urokinase-type plasminogen activator 3.4.21.73 0.660
1q0z AKAAclacinomycin methylesterase RdmC 3.1.1.95 0.660
1qiw DPDCalmodulin / 0.660
1rml NTSFibroblast growth factor 1 / 0.660
1rpw DIDHTH-type transcriptional regulator QacR / 0.660
1u6q 745Urokinase-type plasminogen activator 3.4.21.73 0.660
1vaf ARRNitric oxide synthase, inducible 1.14.13.39 0.660
1w6j R71Lanosterol synthase 5.4.99.7 0.660
2c6h PXICytochrome P450 monooxygenase PikC / 0.660
2cd8 PXICytochrome P450 monooxygenase PikC / 0.660
2pks G44Prothrombin 3.4.21.5 0.660
2q72 IXXNa(+):neurotransmitter symporter (Snf family) / 0.660
2qd3 CHDFerrochelatase, mitochondrial 4.99.1.1 0.660
2qju DSMNa(+):neurotransmitter symporter (Snf family) / 0.660
2y1w 849Histone-arginine methyltransferase CARM1 / 0.660
2yne YNEGlycylpeptide N-tetradecanoyltransferase / 0.660
2z3l PHE_ARG_TYR_LEU_GLYLeucyl/phenylalanyl-tRNA--protein transferase 2.3.2.6 0.660
2z3n PHE_ARG_TYR_LEU_GLYLeucyl/phenylalanyl-tRNA--protein transferase 2.3.2.6 0.660
2zhe 13UProthrombin 3.4.21.5 0.660
2zhw 12UProthrombin 3.4.21.5 0.660
2ziq 26UProthrombin 3.4.21.5 0.660
3biu 10UProthrombin 3.4.21.5 0.660
3biv 11UProthrombin 3.4.21.5 0.660
3dzl 3OCPhenazine biosynthesis protein A/B / 0.660
3h0r ATPAspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B 6.3.5 0.660
3ko0 TFPProtein S100-A4 / 0.660
3lw0 CCXInsulin-like growth factor 1 receptor 2.7.10.1 0.660
3mo2 E67Histone-lysine N-methyltransferase EHMT1 / 0.660
3mo5 E72Histone-lysine N-methyltransferase EHMT1 / 0.660
3psu LJGGag-Pol polyprotein 3.4.23.16 0.660
3q92 XNBKetohexokinase / 0.660
3rqk X2CNitric oxide synthase, brain 1.14.13.39 0.660
3rql X2DNitric oxide synthase, brain 1.14.13.39 0.660
3t5i SER_SER_CMT_FARRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta / 0.660
3v1s 0LHStrictosidine synthase 4.3.3.2 0.660
3zpq XF5Beta-1 adrenergic receptor / 0.660
4b12 C23Glycylpeptide N-tetradecanoyltransferase / 0.660
4bbh YBNGlycylpeptide N-tetradecanoyltransferase / 0.660
4fgj 1PQRibosyldihydronicotinamide dehydrogenase [quinone] / 0.660
4fuf 8UPUrokinase-type plasminogen activator 3.4.21.73 0.660
4fuj 1U9Urokinase-type plasminogen activator 3.4.21.73 0.660
4ge1 TSSBiogenic amine-binding protein / 0.660
4i1r LZUMucosa-associated lymphoid tissue lymphoma translocation protein 1 3.4.22 0.660
4n6h EJ4Delta-type opioid receptor / 0.660
4xp4 COCSodium-dependent dopamine transporter / 0.660
4y57 F63Endothiapepsin 3.4.23.22 0.660
7dfr FOLDihydrofolate reductase 1.5.1.3 0.660
5dhg DGVNociceptin receptor / 0.660
4ea3 0NNNociceptin receptor / 0.660
3cd2 MTXDihydrofolate reductase 1.5.1.3 0.659
3fr2 8CAFatty acid-binding protein, adipocyte / 0.659
4ubs DIFPentalenic acid synthase 1.14.15.11 0.659
1lev CLIFructose-1,6-bisphosphatase 1 3.1.3.11 0.657
4p68 MTXDihydrofolate reductase / 0.657
2fr3 REACellular retinoic acid-binding protein 2 / 0.656
4duh RLIDNA gyrase subunit B / 0.655
4m8e 29VRetinoic acid receptor RXR-alpha / 0.655
1fm9 9CRRetinoic acid receptor RXR-alpha / 0.654
3c6o 2S2Protein TRANSPORT INHIBITOR RESPONSE 1 / 0.654
3oap REARetinoic acid receptor RXR-alpha / 0.654
1chw HXCChalcone synthase 2 2.3.1.74 0.653
3cbs R12Cellular retinoic acid-binding protein 2 / 0.653
3fal REARetinoic acid receptor RXR-alpha / 0.653
4i13 FOLDihydrofolate reductase 1.5.1.3 0.653
4k4j 1O8Retinoic acid receptor RXR-alpha / 0.653
1rdt L79Retinoic acid receptor RXR-alpha / 0.652
2cbr A80Cellular retinoic acid-binding protein 1 / 0.652
2p1u 4TNRetinoic acid receptor RXR-alpha / 0.652
3kp4 MIITranscriptional regulator TcaR / 0.652
4m8h R4MRetinoic acid receptor RXR-alpha / 0.652
5kl9 COAAcyl-CoA thioester hydrolase YbgC 3.1.2 0.652
1dhj MTXDihydrofolate reductase 1.5.1.3 0.651
1fm6 9CRRetinoic acid receptor RXR-alpha / 0.651
1mzn BM6Retinoic acid receptor RXR-alpha / 0.651
2brl POOGenome polyprotein 2.7.7.48 0.651
2j2p SC2Ficolin-2 / 0.651
2yfe YFEPeroxisome proliferator-activated receptor gamma / 0.651
3fr5 I4AFatty acid-binding protein, adipocyte / 0.651
4f0f ACPProbable serine/threonine-protein kinase roco4 2.7.11.1 0.651
1pq6 965Oxysterols receptor LXR-beta / 0.650
2xwy IB8Genome polyprotein 2.7.7.48 0.650
3ipk PMSSurface protein adhesin / 0.650
4a4v YFDPeroxisome proliferator-activated receptor gamma / 0.650
4a4w YFBPeroxisome proliferator-activated receptor gamma / 0.650
4i3p 1CW3-hydroxyanthranilate 3,4-dioxygenase / 0.650
4k6i 9RARetinoic acid receptor RXR-alpha / 0.650
4p66 MTXDihydrofolate reductase / 0.650
5ccc DDFDihydrofolate reductase 1.5.1.3 0.650