scPDB - Distribution of Binding site Similarity values of 4bf9 entry / Site 1

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
4bf9	FMN	tRNA-dihydrouridine(16) synthase

Complex with similar binding sites

PDB ID	HET	Uniprot Name	EC Number	Binding Site Similarity
4bf9	FMN	tRNA-dihydrouridine(16) synthase	/	1.000
4yco	FMN	tRNA-dihydrouridine(16) synthase	/	0.631
4ycp	FMN	tRNA-dihydrouridine(16) synthase	/	0.592
2g24	7IG	Renin	3.4.23.15	0.500
2hs8	FMN	12-oxophytodienoate reductase 3	1.3.1.42	0.495
1ics	FMN	12-oxophytodienoate reductase 1	1.3.1.42	0.491
2hun	NAD	336aa long hypothetical dTDP-glucose 4,6-dehydratase	/	0.487
1icp	FMN	12-oxophytodienoate reductase 1	1.3.1.42	0.483
3tr0	5GP	Guanylate kinase	/	0.481
2g1r	3IG	Renin	3.4.23.15	0.474
5eio	NAP	[LysW]-L-2-aminoadipate 6-phosphate reductase	/	0.474
1vji	FMN	12-oxophytodienoate reductase 1	1.3.1.42	0.473
1xe5	5FE	Plasmepsin-2	3.4.23.39	0.473
2qbu	SAH	Precorrin-2 methyltransferase	/	0.472
2g1n	1IG	Renin	3.4.23.15	0.471
2qs3	UBE	Glutamate receptor ionotropic, kainate 1	/	0.468
1icq	FMN	12-oxophytodienoate reductase 1	1.3.1.42	0.467
4bfz	ZVZ	Pantothenate kinase	2.7.1.33	0.467
1rne	C60	Renin	3.4.23.15	0.465
2abb	FMN	Pentaerythritol tetranitrate reductase	/	0.465
2g22	6IG	Renin	3.4.23.15	0.465
1cnf	FAD	Nitrate reductase [NADH]	1.7.1.1	0.464
3zhs	TD6	Multifunctional 2-oxoglutarate metabolism enzyme	1.2.4.2	0.464
2fxv	5GP	Xanthine phosphoribosyltransferase	2.4.2.22	0.463
3nl6	TPS	Uncharacterized protein	/	0.463
1e0j	ANP	DNA primase/helicase	2.7.7	0.462
1x1a	SAM	C-20 methyltransferase	/	0.461
2eix	FAD	NADH-cytochrome b5 reductase	/	0.461
4ke1	1R6	Beta-secretase 1	3.4.23.46	0.461
2hyd	ADP	Putative multidrug export ATP-binding/permease protein SAV1866	3.6.3	0.460
3qiy	QI1	Botulinum neurotoxin type A	3.4.24.69	0.460
4dpt	AGS	Mevalonate diphosphate decarboxylase	/	0.460
4eb7	PLP	Cysteine desulfurase IscS 2	/	0.460
4xgu	ADP	Putative pachytene checkpoint protein 2	/	0.460
2iko	7IG	Renin	3.4.23.15	0.459
3gka	FMN	N-ethylmaleimide reductase	/	0.458
2il2	LIX	Renin	3.4.23.15	0.457
3aez	GDP	Pantothenate kinase	2.7.1.33	0.457
3d91	REM	Renin	3.4.23.15	0.457
3hgs	FMN	12-oxophytodienoate reductase 3	1.3.1.42	0.457
3p62	FMN	Pentaerythritol tetranitrate reductase	/	0.457
1xva	SAM	Glycine N-methyltransferase	2.1.1.20	0.456
3qiz	QI2	Botulinum neurotoxin type A	3.4.24.69	0.456
1bwl	FMN	NADPH dehydrogenase 1	1.6.99.1	0.455
1kh3	ANP	Argininosuccinate synthase	/	0.455
2hs6	FMN	12-oxophytodienoate reductase 3	1.3.1.42	0.455
3b1d	PLS	BetaC-S lyase	/	0.455
3rba	COD	Phosphopantetheine adenylyltransferase	/	0.455
3v0p	4GW	Histo-blood group ABO system transferase	/	0.455
4a3u	FMN	NADH:flavin oxidoreductase/NADH oxidase	/	0.455
4df2	FMN	NADPH dehydrogenase	/	0.455
4loi	1YC	Stimulator of interferon genes protein	/	0.455
1h50	FMN	Pentaerythritol tetranitrate reductase	/	0.454
1u1g	BBB	Uridine phosphorylase	2.4.2.3	0.454
2a5h	SAM	L-lysine 2,3-aminomutase	5.4.3.2	0.454
1i59	ANP	Chemotaxis protein CheA	2.7.13.3	0.453
2bt4	CA2	3-dehydroquinate dehydratase	4.2.1.10	0.453
2g8y	NAD	Hydroxycarboxylate dehydrogenase B	/	0.453
2ggs	NDP	dTDP-4-dehydrorhamnose reductase	/	0.453
2oap	ANP	Type II secretion system protein (GspE-2)	/	0.453
3f03	FMN	Pentaerythritol tetranitrate reductase	/	0.453
3qj0	QI3	Botulinum neurotoxin type A	3.4.24.69	0.453
4e2d	FMN	Dehydrogenase	/	0.453
1ege	FAD	Medium-chain specific acyl-CoA dehydrogenase, mitochondrial	1.3.8.7	0.452
2ea2	F77	Methionine aminopeptidase 2	/	0.452
2gjl	FMN	Nitronate monooxygenase	1.13.12.16	0.452
3hgo	FMN	12-oxophytodienoate reductase 3	1.3.1.42	0.452
1h63	FMN	Pentaerythritol tetranitrate reductase	/	0.451
3in6	FMN	Uncharacterized protein	/	0.451
2ejz	SAH	Diphthine synthase	/	0.450
2ges	COK	Pantothenate kinase	2.7.1.33	0.449
2zsh	GA3	Gibberellin receptor GID1A	3	0.449
4a6n	FAD	TetX family tetracycline inactivation enzyme	/	0.449
4rnu	FMN	NADPH dehydrogenase 1	1.6.99.1	0.449
1bil	0IU	Renin	3.4.23.15	0.448
1kbo	340	NAD(P)H dehydrogenase [quinone] 1	1.6.5.2	0.448
1x27	ASP_TYR_VAL_HIS_PTR	Tyrosine-protein kinase Lck	2.7.10.2	0.448
2cek	N8T	Acetylcholinesterase	3.1.1.7	0.448
5irn	ADP	Nucleotide binding oligomerization domain containing 2	/	0.448
1xe6	5FP	Plasmepsin-2	3.4.23.39	0.447
1ytm	ATP	Phosphoenolpyruvate carboxykinase (ATP)	/	0.447
2c20	NAD	UDP-glucose 4-epimerase	/	0.447
2o1s	TDP	1-deoxy-D-xylulose-5-phosphate synthase	2.2.1.7	0.447
2q1u	NAD	Putative nucleotide sugar epimerase/ dehydratase	/	0.447
2gv8	NDP	Thiol-specific monooxygenase	1.14.13	0.446
3zoi	M2W	Isopenicillin N synthase	1.21.3.1	0.446
4hmz	18T	dTDP-4-dehydro-6-deoxyglucose 3-epimerase	5.1.3.27	0.446
1toi	HCI	Aspartate aminotransferase	2.6.1.1	0.445
1udb	UFG	UDP-glucose 4-epimerase	5.1.3.2	0.445
1w34	FAD	Ferredoxin--NADP reductase	1.18.1.2	0.445
1x1c	SAH	C-20 methyltransferase	/	0.445
2f3r	G5P	Guanylate kinase	2.7.4.8	0.445
2xfs	J01	Uncharacterized protein	/	0.445
3m1v	COM	Methyl-coenzyme M reductase I subunit alpha	2.8.4.1	0.445
3m1v	COM	Methyl-coenzyme M reductase I subunit beta	2.8.4.1	0.445
3mpi	FAD	Glutaryl-CoA dehydrogenase	1.3.99.32	0.445
2ojt	UBA	Glutamate receptor ionotropic, kainate 1	/	0.444
3k8q	22A	Purine nucleoside phosphorylase	2.4.2.1	0.444
2a94	AP0	L-lactate dehydrogenase	1.1.1.27	0.443
2g1s	4IG	Renin	3.4.23.15	0.443
2wwj	Y28	Lysine-specific demethylase 4A	/	0.443
4ask	K0I	Lysine-specific demethylase 6B	1.14.11	0.443
4lut	DCS	Alanine racemase	/	0.443
1gtr	ATP	Glutamine--tRNA ligase	6.1.1.18	0.442
2a1h	GBN	Branched-chain-amino-acid aminotransferase, mitochondrial	2.6.1.42	0.442
2i65	NAD	ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1	3.2.2.6	0.442
2iku	LIY	Renin	3.4.23.15	0.442
3axk	NDP	Ribulose bisphosphate carboxylase large chain	4.1.1.39	0.442
3fr5	I4A	Fatty acid-binding protein, adipocyte	/	0.442
3hl4	CDC	Choline-phosphate cytidylyltransferase A	/	0.442
3i5z	Z48	Mitogen-activated protein kinase 1	2.7.11.24	0.442
3qt6	2P0	Mevalonate diphosphate decarboxylase	/	0.442
1vyr	FMN	Pentaerythritol tetranitrate reductase	/	0.441
2e0a	ANP	[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial	2.7.11.2	0.441
2fw3	BUI	Carnitine O-palmitoyltransferase 2, mitochondrial	2.3.1.21	0.441
2uxo	TAC	HTH-type transcriptional regulator TtgR	/	0.441
2xug	TZ4	Acetylcholinesterase	3.1.1.7	0.441
2ylr	NAP	Phenylacetone monooxygenase	1.14.13.92	0.441
3int	GDU	UDP-galactopyranose mutase	5.4.99.9	0.441
3muo	ZPR	Prolyl endopeptidase	/	0.441
4gyz	D5M	Tyrosyl-DNA phosphodiesterase 2	3.1.4	0.441
4lh7	1X8	DNA ligase	/	0.441
4rnv	FMN	NADPH dehydrogenase 1	1.6.99.1	0.441
5c1d	12V	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit	/	0.441
1gg5	E09	NAD(P)H dehydrogenase [quinone] 1	1.6.5.2	0.440
1h51	FMN	Pentaerythritol tetranitrate reductase	/	0.440
1h60	STR	Pentaerythritol tetranitrate reductase	/	0.440
1i7p	FAD	NADH-cytochrome b5 reductase 3	1.6.2.2	0.440
1ib0	NAD	NADH-cytochrome b5 reductase 3	1.6.2.2	0.440
2hsd	NAD	3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase	1.1.1.53	0.440
3a1c	ACP	Probable copper-exporting P-type ATPase A	3.6.3.54	0.440
3ehe	NAD	UDP-glucose 4-epimerase (GalE-1)	/	0.440
3te5	NAI	5'-AMP-activated protein kinase subunit gamma	/	0.440