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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
1oe0 TTP Deoxynucleoside kinase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1oe0 TTPDeoxynucleoside kinase / 1.447
2vp0 TTPDeoxynucleoside kinase / 1.377
2jcs TTPDeoxynucleoside kinase / 1.320
2vp2 DGTDeoxynucleoside kinase / 1.131
1zm7 TTPDeoxynucleoside kinase / 1.117
2vp4 DCPDeoxynucleoside kinase / 0.864
2jj8 AZZDeoxynucleoside kinase / 0.726
4mkf AP5Adenylate kinase / 0.720
1p6x THMThymidine kinase / 0.710
1m2o GNPSmall COPII coat GTPase SAR1 3.6.5 0.705
4qm6 GTPMetallophosphoesterase / 0.703
4nyi GNPGTPase HRas / 0.701
1v8k ANPKinesin-like protein KIF2C / 0.700
2rgx AP5Adenylate kinase / 0.700
3i3s GNPGTPase HRas / 0.699
2vqs BVDDeoxynucleoside kinase / 0.697
3dl0 AP5Adenylate kinase / 0.693
4c30 ANPDNA helicase / 0.691
3krf DSTGeranyl diphosphate synthase large subunit / 0.689
3a4l ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.688
3v4f GNPGTPase HRas / 0.688
3rsl GNPGTPase HRas / 0.687
3l8y GNPGTPase HRas / 0.686
4dlz GNPGTPase HRas / 0.686
4dwb 0M7Farnesyl pyrophosphate synthase / 0.686
1ky2 GNPGTP-binding protein YPT7 / 0.685
3oiu GNPGTPase HRas / 0.685
3rs4 GNPGTPase HRas / 0.685
3zfd ANPChromosome-associated kinesin KIF4 / 0.685
4dls GNPGTPase HRas / 0.685
4dlt GNPGTPase HRas / 0.685
5b2z GNPGTPase HRas / 0.685
2rgc GNPGTPase HRas / 0.684
3rs0 GNPGTPase HRas / 0.684
3rs5 GNPGTPase HRas / 0.684
3rs7 GNPGTPase HRas / 0.684
4dlv GNPGTPase HRas / 0.684
4dlx GNPGTPase HRas / 0.684
4l9w GNPGTPase HRas / 0.684
3lbn GNPGTPase HRas / 0.683
4dlw GNPGTPase HRas / 0.683
4m3t ATPDNA-directed DNA polymerase / 0.683
5c03 AGSNon-receptor tyrosine-protein kinase TYK2 2.7.10.2 0.683
2c5l GTPGTPase HRas / 0.682
3vth APCCarbamoyltransferase / 0.682
4hdo GNPRas-related protein Rap-1b / 0.682
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.681
2qaj AP5Adenylate kinase / 0.681
3oiv GNPGTPase HRas / 0.681
3oiw GNPGTPase HRas / 0.681
3vhx GTPADP-ribosylation factor 6 / 0.681
1yu9 GNPRas-related protein Rab-4A / 0.680
3bc1 GNPRas-related protein Rab-27A / 0.680
3m0e ATPTranscriptional regulator (NtrC family) / 0.679
4qxa GTPRas-related protein Rab-9A / 0.679
5i4n ATPTyrosine-protein kinase JAK2 / 0.679
1tu3 GNPRas-related protein Rab-5A / 0.678
3wyf GTPGTP-binding nuclear protein / 0.678
1ank ANPAdenylate kinase / 0.677
1p72 THMThymidine kinase / 0.676
1n5i TMPThymidylate kinase 2.7.4.9 0.675
1p3j AP5Adenylate kinase / 0.675
4ki0 ANPMaltose/maltodextrin import ATP-binding protein MalK / 0.675
1p52 ADPArginine kinase 2.7.3.3 0.674
1n2e APCPantothenate synthetase 6.3.2.1 0.673
4idn GNPAtlastin-1 3.6.5 0.673
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.673
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.672
1khe GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.671
1mmg AGSMyosin-2 heavy chain / 0.671
2jas DTPDeoxyguanosine kinase / 0.671
4idp GNPAtlastin-1 3.6.5 0.670
1k5d GNPGTP-binding nuclear protein Ran / 0.669
3tpt ADPSerine/threonine-protein kinase toxin HipA / 0.669
4tyq AP5Adenylate kinase / 0.669
4fjm DCPDNA-directed DNA polymerase / 0.667
4m3x ATPDNA-directed DNA polymerase / 0.667
1mab ATPATP synthase subunit alpha, mitochondrial / 0.666
3oab DSTGeranyl diphosphate synthase large subunit / 0.666
1s1c GNPTransforming protein RhoA / 0.663
3lbi GNPGTPase HRas / 0.663
4c2u ANPDNA helicase / 0.663
4k81 GTPGTPase HRas / 0.663
1gia GSPGuanine nucleotide-binding protein G(i) subunit alpha-1 / 0.662
1bmf ANPATP synthase subunit alpha, mitochondrial / 0.659
1bmf ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.659
1f9a ATPNicotinamide-nucleotide adenylyltransferase / 0.659
2aky AP5Adenylate kinase / 0.659
2eu8 AP5Adenylate kinase / 0.659
3zia ATPATP synthase subunit alpha, mitochondrial / 0.659
2r5t ANPSerine/threonine-protein kinase Sgk1 2.7.11.1 0.656
1id0 ANPSensor protein PhoQ 2.7.13.3 0.655
1maw ATPTryptophan--tRNA ligase 6.1.1.2 0.655
4d0l GSPRas-related protein Rab-11A / 0.655
4fvq ATPTyrosine-protein kinase JAK2 / 0.655
4js0 GNPCell division control protein 42 homolog / 0.654
4qbg AP5Adenylate kinase / 0.654
3g6x DGTDNA polymerase iota 2.7.7.7 0.653
2cls GTPRho-related GTP-binding protein Rho6 / 0.652
1p7c T5AThymidine kinase / 0.651
2bme GNPRas-related protein Rab-4A / 0.651
3k0f ATPCircadian clock protein kinase KaiC 2.7.11.1 0.651
1jx2 ADPMyosin-2 heavy chain / 0.650
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.650
1xjn DTPVitamin B12-dependent ribonucleotide reductase / 0.650
2fg5 GNPRas-related protein Rab-31 / 0.650
3hpr AP5Adenylate kinase / 0.650
3k8y GNPGTPase HRas / 0.650
3vx4 ATPPutative ABC transporter, ATP-binding protein ComA / 0.650