scPDB - Distribution of Binding site Similarity values of 3u8f 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
3u8f	FGM	Ribosome inactivating protein

Complex with similar binding sites

PDB ID	HET	Uniprot Name	EC Number	Binding Site Similarity
3u8f	FGM	Ribosome inactivating protein	/	1.000
4lwx	MU2	Ribosome inactivating protein	/	0.623
4jtp	ASC	Ribosome inactivating protein	/	0.602
3qji	MGP	Ribosome inactivating protein	/	0.597
5ilw	URI	Ribosome inactivating protein	/	0.568
4emr	MGP	Ribosome inactivating protein	/	0.567
1mrk	FMC	Ribosome-inactivating protein alpha-trichosanthin	3.2.2.22	0.555
4zz6	CTP	Ribosome inactivating protein	/	0.550
1lpc	CMP	Antiviral protein DAP-30	3.2.2.22	0.515
4cdm	FO1	Deoxyribodipyrimidine photolyase	/	0.492
2b8j	ADN	Class B acid phosphatase	3.1.3.2	0.491
1qcj	APT	Antiviral protein I	3.2.2.22	0.489
2g1a	5HG	Class B acid phosphatase	3.1.3.2	0.480
4jxx	ATP	Glutamine--tRNA ligase	6.1.1.18	0.480
1qru	ATP	Glutamine--tRNA ligase	6.1.1.18	0.479
4glx	0XS	DNA ligase	6.5.1.2	0.478
3mjr	AC2	Deoxycytidine kinase	2.7.1.74	0.476
4v0s	2HN	3-dehydroquinate dehydratase	4.2.1.10	0.475
1z5u	CMP	Class B acid phosphatase	/	0.474
2aou	CQA	Histamine N-methyltransferase	2.1.1.8	0.474
4kq6	DLZ	6,7-dimethyl-8-ribityllumazine synthase	/	0.474
1d3d	BZT	Prothrombin	3.4.21.5	0.473
3aiq	HBO	4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic	3.2.1.182	0.471
4j53	1J4	Serine/threonine-protein kinase PLK1	2.7.11.21	0.471
1t13	INI	6,7-dimethyl-8-ribityllumazine synthase 2	/	0.468
3eks	CY9	Actin-5C	/	0.468
3eku	CY9	Actin-5C	/	0.465
1eno	NAD	Enoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic	1.3.1.9	0.464
3b8x	G4M	Putative pyridoxamine 5-phosphate-dependent dehydrase	/	0.464
3f3y	4OA	Bile salt sulfotransferase	2.8.2.14	0.464
4b2g	V1N	Uncharacterized protein	/	0.464
2nr4	FMN	Conserved protein	/	0.463
3zec	ANP	Adenosine monophosphate-protein transferase SoFic	2.7.7.n1	0.461
4rlh	0WE	Enoyl-[acyl-carrier-protein] reductase [NADH]	/	0.461
3nn6	HNK	6-hydroxy-L-nicotine oxidase	/	0.460
4n3r	2GU	Tankyrase-1	2.4.2.30	0.460
4u0s	ADP	Adenosine monophosphate-protein transferase FICD	2.7.7.n1	0.459
1pqc	444	Oxysterols receptor LXR-beta	/	0.458
3uzz	TES	3-oxo-5-beta-steroid 4-dehydrogenase	/	0.458
4b11	7I1	Glycylpeptide N-tetradecanoyltransferase	/	0.458
5dsg	0HK	Muscarinic acetylcholine receptor M4	/	0.458
1i5r	HYC	Estradiol 17-beta-dehydrogenase 1	1.1.1.62	0.457
3biz	61E	Wee1-like protein kinase	2.7.10.2	0.457
1dgb	NDP	Catalase	1.11.1.6	0.456
1u1d	181	Uridine phosphorylase	2.4.2.3	0.456
1ypl	RA8	Prothrombin	3.4.21.5	0.456
3dys	IBM	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	/	0.456
4f3g	KAI	Glutamate receptor 3	/	0.456
4rtb	SAM	Putative thiazole biosynthesis protein ThiH	/	0.456
1obn	ASV	Isopenicillin N synthase	1.21.3.1	0.455
1t4c	COA	Formyl-CoA:oxalate CoA-transferase	/	0.455
2rd2	QSI	Glutamine--tRNA ligase	6.1.1.18	0.455
1p0p	BCH	Cholinesterase	3.1.1.8	0.454
5c6c	CMP	cGMP-dependent protein kinase 2	2.7.11.12	0.454
1euy	QSI	Glutamine--tRNA ligase	6.1.1.18	0.453
4mlp	2CX	Cryptochrome-2	/	0.453
2jl1	NAP	Triphenylmethane reductase	/	0.452
2zev	IPE	Geranylgeranyl pyrophosphate synthase	/	0.452
3zc3	FAD	Ferredoxin--NADP reductase	1.18.1.2	0.452
1e2n	RCA	Thymidine kinase	/	0.451
3rib	SAH	N-lysine methyltransferase SMYD2	/	0.451
4bfy	ZVY	Pantothenate kinase	2.7.1.33	0.451
4dk7	0KS	Oxysterols receptor LXR-beta	/	0.451
4gv0	8ME	Poly [ADP-ribose] polymerase 3	2.4.2.30	0.451
4isg	1FY	Glucokinase	2.7.1.2	0.451
5doz	NDP	JamJ	/	0.451
1c3x	8IG	Purine nucleoside phosphorylase	2.4.2.1	0.450
2fut	H1S	Heparin and heparin-sulfate lyase	/	0.450
2qx7	NAP	Eugenol synthase 1	1.1.1.318	0.450
2xda	JPS	3-dehydroquinate dehydratase	4.2.1.10	0.450
3gn7	3GN	Poly [ADP-ribose] polymerase 1	2.4.2.30	0.450
4d2d	ALA_ALA_ALA	Di-or tripeptide:H+ symporter	/	0.450
1gtr	ATP	Glutamine--tRNA ligase	6.1.1.18	0.449
1vyr	FMN	Pentaerythritol tetranitrate reductase	/	0.449
2g1n	1IG	Renin	3.4.23.15	0.449
2obx	INI	6,7-dimethyl-8-ribityllumazine synthase 2	2.5.1.78	0.449
2rd6	78P	Poly [ADP-ribose] polymerase 1	2.4.2.30	0.449
3buz	TAD	Iota toxin component Ia	/	0.449
3d5w	ADP	Serine/threonine-protein kinase PLK	/	0.449
4gv4	MEJ	Poly [ADP-ribose] polymerase 3	2.4.2.30	0.449
1lbb	KAI	Glutamate receptor 2	/	0.448
2jj2	ANP	ATP synthase subunit beta, mitochondrial	3.6.3.14	0.448
3p8i	FMN	Pentaerythritol tetranitrate reductase	/	0.448
4xt8	TMQ	Possible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc	/	0.448
1nqu	RDL	6,7-dimethyl-8-ribityllumazine synthase	2.5.1.78	0.447
1qti	GNT	Acetylcholinesterase	3.1.1.7	0.447
2w6z	L21	Biotin carboxylase	6.3.4.14	0.447
2xiq	5AD	Methylmalonyl-CoA mutase, mitochondrial	/	0.447
3zv7	NHG	Acetylcholinesterase	3.1.1.7	0.447
2cek	N8T	Acetylcholinesterase	3.1.1.7	0.446
3nyt	ULP	UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase	2.6.1.98	0.446
4a95	9MT	Glycylpeptide N-tetradecanoyltransferase	/	0.446
4jxz	ATP	Glutamine--tRNA ligase	6.1.1.18	0.446
4xbf	FAD	Lysine-specific histone demethylase 1A	1	0.446
1dr4	HBI	Dihydrofolate reductase	1.5.1.3	0.445
1toi	HCI	Aspartate aminotransferase	2.6.1.1	0.445
1u1f	183	Uridine phosphorylase	2.4.2.3	0.445
1vot	HUP	Acetylcholinesterase	3.1.1.7	0.445
2bn4	FMN	NADPH--cytochrome P450 reductase	/	0.445
2imk	GTX	AGAP009194-PA	/	0.445
2jiz	ANP	ATP synthase subunit beta, mitochondrial	3.6.3.14	0.445
3qtv	06P	Prothrombin	3.4.21.5	0.445
4bqy	FNT	Egl nine homolog 1	/	0.445
5a88	ADP	Riboflavin biosynthesis protein RibF	2.7.1.26	0.445
1a69	FMB	Purine nucleoside phosphorylase DeoD-type	/	0.444
2a5k	AZP	Replicase polyprotein 1ab	3.4.22	0.444
2h44	7CA	cGMP-specific 3',5'-cyclic phosphodiesterase	/	0.444
2pj4	414	Carboxypeptidase B	/	0.444
3gjw	GJW	Poly [ADP-ribose] polymerase 1	2.4.2.30	0.444
3ozd	4CT	S-methyl-5'-thioadenosine phosphorylase	/	0.444
3uzw	NAP	3-oxo-5-beta-steroid 4-dehydrogenase	/	0.444
4f0e	0RU	Poly [ADP-ribose] polymerase 15	2.4.2.30	0.444
4jsr	1NQ	NAD-dependent protein deacetylase sirtuin-3, mitochondrial	3.5.1	0.444
1nzy	BCA	4-chlorobenzoyl coenzyme A dehalogenase	3.8.1.7	0.443
1pq9	44B	Oxysterols receptor LXR-beta	/	0.443
2a59	LMZ	6,7-dimethyl-8-ribityllumazine synthase	2.5.1.78	0.443
2ed3	SAH	Diphthine synthase	/	0.443
2g8y	NAD	Hydroxycarboxylate dehydrogenase B	/	0.443
2xf3	J01	Uncharacterized protein	/	0.443
2y67	N21	UDP-N-acetylmuramoylalanine--D-glutamate ligase	6.3.2.9	0.443
2z4w	749	Geranylgeranyl pyrophosphate synthase	/	0.443
3abx	RCB	Glucanase	/	0.443
3nu0	3TU	Dihydrofolate reductase	1.5.1.3	0.443
4u14	0HK	Muscarinic acetylcholine receptor M3	/	0.443
1ja1	FMN	NADPH--cytochrome P450 reductase	/	0.442
1kyv	RBF	6,7-dimethyl-8-ribityllumazine synthase	2.5.1.78	0.442
2w6q	OA5	Biotin carboxylase	6.3.4.14	0.442
2xje	U5P	Cytosolic purine 5'-nucleotidase	3.1.3.5	0.442
2xnv	VU3	Soluble acetylcholine receptor	/	0.442
3jyo	NAD	Quinate/shikimate dehydrogenase (NAD(+))	/	0.442
4e90	7RG	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	/	0.442
5fm7	ADP	RuvB-like helicase	/	0.442
2ejz	SAH	Diphthine synthase	/	0.441
2g28	TDK	Pyruvate dehydrogenase E1 component	1.2.4.1	0.441
2vi5	Y19	6,7-dimethyl-8-ribityllumazine synthase	2.5.1.78	0.441
2zev	B71	Geranylgeranyl pyrophosphate synthase	/	0.441
3gb4	D3M	DdmC	/	0.441
3qeo	LLT	Deoxycytidine kinase	2.7.1.74	0.441
4a3u	FMN	NADH:flavin oxidoreductase/NADH oxidase	/	0.441
4lut	DCS	Alanine racemase	/	0.441
1d3p	BT3	Prothrombin	3.4.21.5	0.440
1h60	STR	Pentaerythritol tetranitrate reductase	/	0.440
1pkf	EPD	Epothilone C/D epoxidase	1.14	0.440
1x27	ASP_TYR_VAL_HIS_PTR	Tyrosine-protein kinase Lck	2.7.10.2	0.440
2re8	GSU	Glutamine--tRNA ligase	6.1.1.18	0.440
3fzn	D7K	Benzoylformate decarboxylase	4.1.1.7	0.440
3ppk	FNI	Serine/threonine-protein kinase B-raf	2.7.11.1	0.440
4gh6	LUO	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	/	0.440