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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
1jsz NDM Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 2.1.1.57

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1n6m ADPProtein claret segregational / 0.744
1ohh ANPATP synthase subunit alpha, mitochondrial / 0.744
1ohh ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.744
1onp FOM1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.744
1r8b ATPCCA-adding enzyme 2.7.7.72 0.744
1u26 IHSMyo-inositol hexaphosphate phosphohydrolase / 0.744
1v8k ANPKinesin-like protein KIF2C / 0.744
1ybu APCProbable lignin peroxidase LipJ / 0.744
2e91 ZOLGeranylgeranyl pyrophosphate synthase / 0.744
2gyu HI6Acetylcholinesterase 3.1.1.7 0.744
2oem 1AE2,3-diketo-5-methylthiopentyl-1-phosphate enolase 5.3.2.5 0.744
2qf2 GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.744
2vd7 PD2Lysine-specific demethylase 4A 1.14.11 0.744
2zfi ADPKinesin-like protein KIF1A / 0.744
2zsb ADPPantothenate kinase 2.7.1.33 0.744
3af3 GCPPantothenate kinase 2.7.1.33 0.744
3ar5 TM1Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 3.6.3.8 0.744
3au2 DGTDNA polymerase beta family (X family) / 0.744
3cob ADPKinesin heavy chain-like protein / 0.744
3l1c ADPProtein claret segregational / 0.744
3lm9 ADPPutative fructokinase 2.7.1.4 0.744
3ppo DCKGlycine betaine/carnitine/choline-binding protein OpuCC / 0.744
3ta2 ATPNitrogen regulatory protein P-II (GlnB-3) / 0.744
3zcb ATPAdenosine monophosphate-protein transferase VbhT 2.7.7.n1 0.744
4a8m GTPRNA-directed RNA polymerase 2.7.7.48 0.744
4at8 ATPInterleukin enhancer-binding factor 2 / 0.744
4blt APCNTPase P4 / 0.744
4cei ANPATP-dependent helicase/deoxyribonuclease subunit B 3.1 0.744
4e09 ACPPlasmid partitioning protein ParF / 0.744
4fdu IHSPutative multiple inositol polyphosphate histidine phosphatase 1 / 0.744
4ie5 MD6Alpha-ketoglutarate-dependent dioxygenase FTO / 0.744
4lxl PD2Lysine-specific demethylase 4B 1.14.11 0.744
4rf9 AGSArginine kinase 2.7.3.3 0.744
4uz6 SCRPalmitoleoyl-protein carboxylesterase NOTUM / 0.744
5egh PCEctonucleotide pyrophosphatase/phosphodiesterase family member 6 / 0.744
1jsz NDMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 2.1.1.57 0.697
1qk3 5GPHypoxanthine-guanine-xanthine phosphoribosyltransferase 2.4.2.22 0.661
3cb2 GDPTubulin gamma-1 chain / 0.661
1a5u ATPPyruvate kinase PKM 2.7.1.40 0.660
1i4l GDPRas-related C3 botulinum toxin substrate 1 / 0.660
1phq FPE2-dehydro-3-deoxyphosphooctonate aldolase 2.5.1.55 0.660
2e20 B4PPropionate kinase / 0.660
3adc ANPL-seryl-tRNA(Sec) kinase 2.7.1.164 0.660
3ar6 12DSarcoplasmic/endoplasmic reticulum calcium ATPase 1 3.6.3.8 0.660
3asj XYMHomoisocitrate dehydrogenase / 0.660
3u9e COALmo1369 protein / 0.660
3w2w ATPCRISPR system Cmr subunit Cmr2 / 0.660
3w8r ACPUridine kinase / 0.660
3zlm ANPAdenosine monophosphate-protein transferase NmFic 2.7.7.n1 0.660
4co0 ADPNitrogen regulatory protein P-II 1 / 0.660
4hdh ATPGenome polyprotein 2.7.7.48 0.660
4usj ATPNitrogen regulatory protein PII / 0.660
5erm 210Fusicoccadiene synthase 4.2.3.43 0.660
5i67 GDPPhosphoenolpyruvate carboxykinase [GTP] / 0.660
4yj2 GTPTubulin alpha-1B chain / 0.658
2y4l GDPUncharacterized protein / 0.653
2y4k GDPUncharacterized protein / 0.652