scPDB - Distribution of Binding site Similarity values of 2j5b entry / Site 2

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
2j5b	TYE	Tyrosine--tRNA ligase	6.1.1.1

Complex with similar binding sites

PDB ID	HET	Uniprot Name	EC Number	Binding Site Similarity
2j5b	TYE	Tyrosine--tRNA ligase	6.1.1.1	1.000
3p0j	TYE	Putative tyrosyl-tRNA synthetase	/	0.528
1drh	NAP	Dihydrofolate reductase	1.5.1.3	0.483
5hg0	SAM	Pantothenate synthetase	/	0.478
2qn3	F55	Glycogen phosphorylase, muscle form	2.4.1.1	0.477
3zxi	TYA	Tyrosine--tRNA ligase, mitochondrial	6.1.1.1	0.477
2iyf	ERY	Oleandomycin glycosyltransferase	2.4.1	0.473
4wso	NAD	Probable nicotinate-nucleotide adenylyltransferase	/	0.472
1rct	NOS	Purine nucleoside phosphorylase	2.4.2.1	0.469
3cib	314	Beta-secretase 1	3.4.23.46	0.469
2nni	MTK	Cytochrome P450 2C8	/	0.468
1jil	485	Tyrosine--tRNA ligase	/	0.467
1kp2	ATP	Argininosuccinate synthase	6.3.4.5	0.465
1pwy	AC2	Purine nucleoside phosphorylase	2.4.2.1	0.465
2p83	MR0	Beta-secretase 1	3.4.23.46	0.465
1gzu	NMN	Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1	2.7.7.1	0.464
1jqd	SAH	Histamine N-methyltransferase	2.1.1.8	0.463
3lpk	Z76	Beta-secretase 1	3.4.23.46	0.463
4rvg	TYD	D-mycarose 3-C-methyltransferase	/	0.462
2g94	ZPQ	Beta-secretase 1	3.4.23.46	0.461
3vf3	0GS	Beta-secretase 1	3.4.23.46	0.461
4x7u	ZM3	Mycinamicin III 3''-O-methyltransferase	2.1.1.237	0.461
1ib0	NAD	NADH-cytochrome b5 reductase 3	1.6.2.2	0.460
4dbz	NDP	Putative ketoacyl reductase	1.3.1	0.460
1ia3	TQ5	Dihydrofolate reductase	1.5.1.3	0.459
1owe	675	Urokinase-type plasminogen activator	3.4.21.73	0.459
2a94	AP0	L-lactate dehydrogenase	1.1.1.27	0.459
3inv	NDP	Bifunctional dihydrofolate reductase-thymidylate synthase	1.5.1.3	0.459
3em0	CHD	Fatty acid-binding protein 6, ileal (gastrotropin)	/	0.458
1dds	MTX	Dihydrofolate reductase	1.5.1.3	0.457
2xfk	AA9	Beta-secretase 1	3.4.23.46	0.457
3dga	NDP	Bifunctional dihydrofolate reductase-thymidylate synthase	1.5.1.3	0.457
3etd	NDP	Glutamate dehydrogenase 1, mitochondrial	1.4.1.3	0.457
4yvj	SFG	tRNA (guanine-N(1)-)-methyltransferase	2.1.1.228	0.457
1n77	ATP	Glutamate--tRNA ligase	6.1.1.17	0.456
1xe6	5FP	Plasmepsin-2	3.4.23.39	0.456
2vig	FAD	Short-chain specific acyl-CoA dehydrogenase, mitochondrial	1.3.8.1	0.456
1gj4	132	Prothrombin	3.4.21.5	0.455
3qt6	2P0	Mevalonate diphosphate decarboxylase	/	0.455
1i0s	FMN	Ferric-chelate reductase (NAD(P)H)	/	0.454
1jik	545	Tyrosine--tRNA ligase	/	0.454
1nuu	NAD	Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3	/	0.454
1rx1	NAP	Dihydrofolate reductase	1.5.1.3	0.454
2d29	FAD	Acyl-CoA dehydrogenase	/	0.454
2pid	YSA	Tyrosine--tRNA ligase, mitochondrial	6.1.1.1	0.454
3mpi	FAD	Glutaryl-CoA dehydrogenase	1.3.99.32	0.454
1udb	UFG	UDP-glucose 4-epimerase	5.1.3.2	0.453
2dvl	FAD	Acyl-CoA dehydrogenase	/	0.453
2f3e	AXQ	Beta-secretase 1	3.4.23.46	0.453
2g25	TDK	Pyruvate dehydrogenase E1 component	1.2.4.1	0.453
3img	BZ2	Pantothenate synthetase	6.3.2.1	0.453
4hp8	NAP	2-deoxy-D-gluconate 3-dehydrogenase	/	0.453
1t2c	NAI	L-lactate dehydrogenase	1.1.1.27	0.452
3lpi	Z74	Beta-secretase 1	3.4.23.46	0.452
3ohh	3HH	Beta-secretase 1	3.4.23.46	0.452
4an4	DUD	Putative glycosyl transferase	/	0.452
4nd3	NAD	Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase	/	0.452
1dr2	TAP	Dihydrofolate reductase	1.5.1.3	0.451
2ex1	C5P	Alpha-2,3/2,6-sialyltransferase/sialidase	/	0.451
2il2	LIX	Renin	3.4.23.15	0.451
3ivx	FG6	Pantothenate synthetase	6.3.2.1	0.451
4bup	SAM	Histone-lysine N-methyltransferase KMT5B	2.1.1.43	0.451
4dpi	0N1	Beta-secretase 1	3.4.23.46	0.451
4kgk	GTP	Uncharacterized protein	/	0.451
1a9z	UPG	UDP-glucose 4-epimerase	5.1.3.2	0.450
1uda	UFG	UDP-glucose 4-epimerase	5.1.3.2	0.450
1xdp	ATP	Polyphosphate kinase	/	0.450
3f03	FMN	Pentaerythritol tetranitrate reductase	/	0.450
4a86	2AN	Major pollen allergen Bet v 1-A	/	0.450
4jnk	NAI	L-lactate dehydrogenase A chain	1.1.1.27	0.450
4k8s	1QT	Beta-secretase 1	3.4.23.46	0.450
4qmp	DKI	Serine/threonine-protein kinase 24	2.7.11.1	0.450
1ia4	TQ6	Dihydrofolate reductase	1.5.1.3	0.449
3h2s	NDP	Putative NADH-flavin reductase	/	0.449
3kjs	NAP	Bifunctional dihydrofolate reductase-thymidylate synthase	/	0.449
3nsh	957	Beta-secretase 1	3.4.23.46	0.449
4i0i	957	Beta-secretase 1	3.4.23.46	0.449
4trn	NAD	Enoyl-[acyl-carrier-protein] reductase [NADH]	1.3.1.9	0.449
1x1a	SAM	C-20 methyltransferase	/	0.448
1xs7	MMI	Beta-secretase 1	3.4.23.46	0.448
2hiz	LIJ	Beta-secretase 1	3.4.23.46	0.448
2ktd	PUC	Prostaglandin-H2 D-isomerase	5.3.99.2	0.448
3ict	FAD	Coenzyme A disulfide reductase	/	0.448
3ixk	929	Beta-secretase 1	3.4.23.46	0.448
3k5f	AYH	Beta-secretase 1	3.4.23.46	0.448
3r83	Z14	Cyclin-dependent kinase 2	2.7.11.22	0.448
4fse	0VA	Beta-secretase 1	3.4.23.46	0.448
1rfu	ADP	Pyridoxal kinase	2.7.1.35	0.447
2cv2	GSU	Glutamate--tRNA ligase	6.1.1.17	0.447
2fxv	5GP	Xanthine phosphoribosyltransferase	2.4.2.22	0.447
2ilv	C5P	Alpha-2,3/2,6-sialyltransferase/sialidase	/	0.447
2iqg	F2I	Beta-secretase 1	3.4.23.46	0.447
2vnm	CM8	Beta-secretase 1	3.4.23.46	0.447
2whq	HI6	Acetylcholinesterase	3.1.1.7	0.447
3cgt	BCD	Cyclomaltodextrin glucanotransferase	2.4.1.19	0.447
3g2h	KOT	Glycogen phosphorylase, muscle form	2.4.1.1	0.447
3k5g	BJC	Beta-secretase 1	3.4.23.46	0.447
3skg	PB8	Beta-secretase 1	3.4.23.46	0.447
4a6r	TA8	Probable aminotransferase	/	0.447
4uwm	FMN	3,6-diketocamphane 1,6 monooxygenase	1.14.13	0.447
1fcb	FMN	Cytochrome b2, mitochondrial	1.1.2.3	0.446
2z3n	PHE_ARG_TYR_LEU_GLY	Leucyl/phenylalanyl-tRNA--protein transferase	2.3.2.6	0.446
3cic	316	Beta-secretase 1	3.4.23.46	0.445
3lpj	Z75	Beta-secretase 1	3.4.23.46	0.445
5dw6	0T1	Succinyl-CoA:acetate CoA-transferase	/	0.445
2g1s	4IG	Renin	3.4.23.15	0.444
2vij	C44	Beta-secretase 1	3.4.23.46	0.444
2wns	OMP	Uridine 5'-monophosphate synthase	2.4.2.10	0.444
3mpj	FAD	Glutaryl-CoA dehydrogenase	1.3.99.32	0.444
3v2u	ATP	Protein GAL3	/	0.444
4ewo	996	Beta-secretase 1	3.4.23.46	0.444
4u03	GTP	Cyclic GMP-AMP synthase	/	0.444
4u97	STU	Interleukin-1 receptor-associated kinase 4	2.7.11.1	0.444
1dr3	TAP	Dihydrofolate reductase	1.5.1.3	0.443
2iko	7IG	Renin	3.4.23.15	0.443
2qs3	UBE	Glutamate receptor ionotropic, kainate 1	/	0.443
3tjz	GNP	ADP-ribosylation factor 1	/	0.443
4b66	NAP	L-ornithine N(5)-monooxygenase	/	0.443
4fco	0U4	Beta-secretase 1	3.4.23.46	0.443
1dr5	NAP	Dihydrofolate reductase	1.5.1.3	0.442
1gg5	E09	NAD(P)H dehydrogenase [quinone] 1	1.6.5.2	0.442
1kh3	ANP	Argininosuccinate synthase	/	0.442
2is0	I03	Beta-secretase 1	3.4.23.46	0.442
4eu9	COA	Succinyl-CoA:acetate CoA-transferase	/	0.442
4i1n	FOL	Dihydrofolate reductase	1.5.1.3	0.442
5f8e	SAH	Possible transcriptional regulatory protein	/	0.442
1kp3	ATP	Argininosuccinate synthase	6.3.4.5	0.441
1u7h	NAD	Putative ornithine cyclodeaminase	/	0.441
2abb	FMN	Pentaerythritol tetranitrate reductase	/	0.441
2c1b	CQP	cAMP-dependent protein kinase catalytic subunit alpha	2.7.11.11	0.441
3ms4	21N	Glycogen phosphorylase, muscle form	2.4.1.1	0.441
1bim	0QB	Renin	3.4.23.15	0.440
1i7g	AZ2	Peroxisome proliferator-activated receptor alpha	/	0.440
1z7y	AA5	Cysteine synthase 1	2.5.1.47	0.440
2hun	NAD	336aa long hypothetical dTDP-glucose 4,6-dehydratase	/	0.440
2p2q	PRX	Acetyl-coenzyme A synthetase	/	0.440
2zjm	F1M	Beta-secretase 1	3.4.23.46	0.440
3dv5	BAV	Beta-secretase 1	3.4.23.46	0.440
3e8n	VRA	Dual specificity mitogen-activated protein kinase kinase 1	2.7.12.2	0.440
3jsk	AHZ	Thiamine thiazole synthase	/	0.440
4djh	JDC	Kappa-type opioid receptor	/	0.440