scPDB - Distribution of Binding site Similarity values of 3duf entry / Site 4

Distribution of Binding site similarity measured by Shaper

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Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :

PDB ID	HET	Uniprot Name	EC Number
3duf	R1T	Pyruvate dehydrogenase E1 component subunit alpha	1.2.4.1

Complex with similar binding sites

PDB ID	HET	Uniprot Name	EC Number	Binding Site Similarity
3duf	R1T	Pyruvate dehydrogenase E1 component subunit alpha	1.2.4.1	1.000
3duf	R1T	Pyruvate dehydrogenase E1 component subunit beta	1.2.4.1	1.000
2j9f	THV	2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial	1.2.4.4	0.559
2j9f	THV	2-oxoisovalerate dehydrogenase subunit beta, mitochondrial	1.2.4.4	0.559
3wv9	FEG	Hmd co-occurring protein HcgE	/	0.498
3dva	TPW	Pyruvate dehydrogenase E1 component subunit alpha	1.2.4.1	0.495
3dva	TPW	Pyruvate dehydrogenase E1 component subunit beta	1.2.4.1	0.495
3dv0	TPW	Pyruvate dehydrogenase E1 component subunit alpha	1.2.4.1	0.490
3dv0	TPW	Pyruvate dehydrogenase E1 component subunit beta	1.2.4.1	0.490
3zht	TD9	Multifunctional 2-oxoglutarate metabolism enzyme	1.2.4.2	0.489
3qeo	LLT	Deoxycytidine kinase	2.7.1.74	0.488
2zi6	3D1	Deoxycytidine kinase	2.7.1.74	0.478
2rlc	CHD	Choloylglycine hydrolase	3.5.1.24	0.474
1tka	N3T	Transketolase 1	2.2.1.1	0.471
2re8	GSU	Glutamine--tRNA ligase	6.1.1.18	0.470
4bby	FAD	Alkyldihydroxyacetonephosphate synthase, peroxisomal	2.5.1.26	0.470
2rd2	QSI	Glutamine--tRNA ligase	6.1.1.18	0.469
4bb2	STR	Corticosteroid-binding globulin	/	0.468
2q1s	NAI	Putative nucleotide sugar epimerase/ dehydratase	/	0.467
3h3r	14H	Collagen type IV alpha-3-binding protein	/	0.467
3zhv	TDW	Multifunctional 2-oxoglutarate metabolism enzyme	1.2.4.2	0.467
2v95	HCY	Corticosteroid-binding globulin	/	0.466
3dyl	IBM	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	/	0.465
1eve	E20	Acetylcholinesterase	3.1.1.7	0.464
1h50	FMN	Pentaerythritol tetranitrate reductase	/	0.464
3h3q	H13	Collagen type IV alpha-3-binding protein	/	0.464
3jsi	WTC	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	/	0.464
4jxx	ATP	Glutamine--tRNA ligase	6.1.1.18	0.463
2j3q	TFL	Acetylcholinesterase	3.1.1.7	0.462
3jsw	JAR	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	/	0.462
1yhn	GTP	Ras-related protein Rab-7a	/	0.461
4a81	DXC	Major pollen allergen Bet v 1-A	/	0.461
2xlr	FAD	Putative flavin-containing monooxygenase	/	0.460
3exh	TPP	Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial	1.2.4.1	0.460
3exh	TPP	Pyruvate dehydrogenase E1 component subunit beta, mitochondrial	1.2.4.1	0.460
1qrs	ATP	Glutamine--tRNA ligase	6.1.1.18	0.459
2xiq	5AD	Methylmalonyl-CoA mutase, mitochondrial	/	0.459
4j8t	DOG	Uncharacterized PhzA/B-like protein PA3332	/	0.459
2ivi	ACW	Isopenicillin N synthase	1.21.3.1	0.458
2jb4	A14	Isopenicillin N synthase	1.21.3.1	0.458
3dyq	IBM	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	/	0.457
3mjr	AC2	Deoxycytidine kinase	2.7.1.74	0.457
4n3r	2GU	Tankyrase-1	2.4.2.30	0.457
3zhu	TD8	Multifunctional 2-oxoglutarate metabolism enzyme	1.2.4.2	0.456
4rvg	TYD	D-mycarose 3-C-methyltransferase	/	0.456
1kw0	H4B	Phenylalanine-4-hydroxylase	1.14.16.1	0.455
2w6c	BM4	Acetylcholinesterase	3.1.1.7	0.455
2xq0	BES	Leukotriene A-4 hydrolase homolog	3.3.2.6	0.455
1bk0	ACV	Isopenicillin N synthase	1.21.3.1	0.454
3n3z	IBM	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	/	0.454
2qim	ZEA	Class 10 plant pathogenesis-related protein	/	0.453
2vbd	V10	Isopenicillin N synthase	1.21.3.1	0.453
3h3t	16H	Collagen type IV alpha-3-binding protein	/	0.453
3oqf	S51	Renin	3.4.23.15	0.453
2o1s	TDP	1-deoxy-D-xylulose-5-phosphate synthase	2.2.1.7	0.452
3bi5	FAD	Polyamine oxidase FMS1	/	0.452
3dy8	IBM	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	/	0.452
4bc7	FAD	Alkyldihydroxyacetonephosphate synthase, peroxisomal	2.5.1.26	0.452
3em0	CHD	Fatty acid-binding protein 6, ileal (gastrotropin)	/	0.451
4do3	0LA	Fatty-acid amide hydrolase 1	3.5.1.99	0.451
4mlp	2CX	Cryptochrome-2	/	0.451
1vg8	GNP	Ras-related protein Rab-7a	/	0.450
2g1r	3IG	Renin	3.4.23.15	0.450
2gil	GTP	Ras-related protein Rab-6A	/	0.450
4bb3	KKA	Isopenicillin N synthase	1.21.3.1	0.450
1qtq	QSI	Glutamine--tRNA ligase	6.1.1.18	0.449
1xl8	152	Peroxisomal carnitine O-octanoyltransferase	2.3.1.137	0.449
3qi4	IBM	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	/	0.449
4arb	C57	Acetylcholinesterase	3.1.1.7	0.449
4n3l	2FN	Prothrombin	3.4.21.5	0.449
1pwy	AC2	Purine nucleoside phosphorylase	2.4.2.1	0.448
3f8w	ADN	Purine nucleoside phosphorylase	/	0.448
3u9f	CLM	Chloramphenicol acetyltransferase	2.3.1.28	0.448
3v0p	4GW	Histo-blood group ABO system transferase	/	0.448
1hb3	SCV	Isopenicillin N synthase	1.21.3.1	0.447
1nzq	162	Prothrombin	3.4.21.5	0.447
2dxi	ATP	Glutamate--tRNA ligase	6.1.1.17	0.447
2rqf	JH3	Hemolymph juvenile hormone binding protein	/	0.447
2v57	PRL	TetR family transcriptional regulator	/	0.447
2v58	LZJ	Biotin carboxylase	6.3.4.14	0.447
3dys	IBM	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	/	0.447
3uzz	ASD	3-oxo-5-beta-steroid 4-dehydrogenase	/	0.447
4c2z	646	Glycylpeptide N-tetradecanoyltransferase 1	/	0.447
1gtr	ATP	Glutamine--tRNA ligase	6.1.1.18	0.446
3cot	STR	3-oxo-5-beta-steroid 4-dehydrogenase	/	0.446
3k3h	BYE	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	/	0.446
4a83	DXC	Major pollen allergen Bet v 1-A	/	0.446
1trk	TPP	Transketolase 1	2.2.1.1	0.445
1w88	TDP	Pyruvate dehydrogenase E1 component subunit alpha	1.2.4.1	0.445
1w88	TDP	Pyruvate dehydrogenase E1 component subunit beta	1.2.4.1	0.445
1xtr	GNP	GTP-binding protein Rheb	/	0.445
2il2	LIX	Renin	3.4.23.15	0.445
4bfz	ZVZ	Pantothenate kinase	2.7.1.33	0.445
4jlm	1NN	Deoxycytidine kinase	2.7.1.74	0.445
4psb	GA3	Cytokinin-specific binding protein	/	0.445
4x7u	ZM3	Mycinamicin III 3''-O-methyltransferase	2.1.1.237	0.445
1obn	ASV	Isopenicillin N synthase	1.21.3.1	0.444
1zgb	A1E	Acetylcholinesterase	3.1.1.7	0.444
2g22	6IG	Renin	3.4.23.15	0.444
2gyu	HI6	Acetylcholinesterase	3.1.1.7	0.444
3fkt	SII	Beta-secretase 1	3.4.23.46	0.444
3p8i	FMN	Pentaerythritol tetranitrate reductase	/	0.444
4xgu	ADP	Putative pachytene checkpoint protein 2	/	0.444
1w19	T1P	6,7-dimethyl-8-ribityllumazine synthase	2.5.1.78	0.443
3g5s	FAD	Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO	/	0.443
1itz	TPP	Transketolase, chloroplastic	2.2.1.1	0.442
1pqc	444	Oxysterols receptor LXR-beta	/	0.442
1rt9	IMH	Purine nucleoside phosphorylase	2.4.2.1	0.442
1txt	CAA	HMG-CoA synthase	/	0.442
2gjn	FMN	Nitronate monooxygenase	1.13.12.16	0.442
2yy2	IBM	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	/	0.442
2zi5	3L1	Deoxycytidine kinase	2.7.1.74	0.442
3c3x	NAP	Eugenol synthase 1	1.1.1.318	0.442
3e5h	GNP	Ras-related protein Rab-28	/	0.442
4iji	99T	Glutathione S-transferase-like protein YibF	/	0.442
5irn	ADP	Nucleotide binding oligomerization domain containing 2	/	0.442
1h22	E10	Acetylcholinesterase	3.1.1.7	0.441
1h63	FMN	Pentaerythritol tetranitrate reductase	/	0.441
1t4v	14A	Prothrombin	3.4.21.5	0.441
1zgi	382	Prothrombin	3.4.21.5	0.441
2a0y	DIH	Purine nucleoside phosphorylase	2.4.2.1	0.441
2iko	7IG	Renin	3.4.23.15	0.441
2q1t	NAD	Putative nucleotide sugar epimerase/ dehydratase	/	0.441
2w6p	OA4	Biotin carboxylase	6.3.4.14	0.441
3sqz	COA	Putative hydroxymethylglutaryl-CoA synthase	/	0.441
4a86	H35	Major pollen allergen Bet v 1-A	/	0.441
1rzu	ADP	Glycogen synthase 1	2.4.1.21	0.440
1wnz	2VA	Isoleucine--tRNA ligase	6.1.1.5	0.440
2r5n	TPP	Transketolase 1	/	0.440
3bk2	U5P	Ribonuclease J	/	0.440
3eu5	GBO	Protein farnesyltransferase subunit beta	2.5.1.58	0.440
3g72	A6T	Renin	3.4.23.15	0.440
4bao	MVF	Prothrombin	3.4.21.5	0.440
4kby	C2E	Stimulator of interferon genes protein	/	0.440