scPDB - Distribution of Binding site Similarity values of 2dxd 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
2dxd	ANP	Nucleoside diphosphate kinase	2.7.4.6

Complex with similar binding sites

PDB ID	HET	Uniprot Name	EC Number	Binding Site Similarity
2dxd	ANP	Nucleoside diphosphate kinase	2.7.4.6	1.000
3q8u	ADP	Nucleoside diphosphate kinase	/	0.614
1nhk	CMP	Nucleoside diphosphate kinase	2.7.4.6	0.586
4hr2	ADP	Nucleoside diphosphate kinase	/	0.572
1wkl	ATP	Nucleoside diphosphate kinase	/	0.529
2dxf	GNP	Nucleoside diphosphate kinase	2.7.4.6	0.506
3mpi	FAD	Glutaryl-CoA dehydrogenase	1.3.99.32	0.500
4bfz	ZVZ	Pantothenate kinase	2.7.1.33	0.490
1ld8	U49	Protein farnesyltransferase subunit beta	2.5.1.58	0.481
3gwd	NAP	Cyclohexanone monooxygenase	/	0.481
1ni1	HFP	Protein farnesyltransferase subunit beta	2.5.1.58	0.476
2ylr	NAP	Phenylacetone monooxygenase	1.14.13.92	0.476
4isk	1JY	Thymidylate synthase	/	0.476
1bux	PPS	Nucleoside diphosphate kinase, cytosolic	2.7.4.6	0.474
1h36	R88	Squalene--hopene cyclase	4.2.1.129	0.474
3zei	AWH	O-acetylserine sulfhydrylase	/	0.473
3eu5	GBO	Protein farnesyltransferase subunit beta	2.5.1.58	0.472
1siq	FAD	Glutaryl-CoA dehydrogenase, mitochondrial	1.3.8.6	0.471
2dvl	FAD	Acyl-CoA dehydrogenase	/	0.471
2d29	FAD	Acyl-CoA dehydrogenase	/	0.470
1ni1	2C5	Protein farnesyltransferase subunit beta	2.5.1.58	0.468
4hmz	18T	dTDP-4-dehydro-6-deoxyglucose 3-epimerase	5.1.3.27	0.467
2hve	ADP	Nucleoside diphosphate kinase A	2.7.4.6	0.466
3tjz	GNP	ADP-ribosylation factor 1	/	0.465
1pqc	444	Oxysterols receptor LXR-beta	/	0.464
1n95	HFP	Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha	/	0.463
1n95	HFP	Protein farnesyltransferase subunit beta	2.5.1.58	0.463
1nup	NMN	Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3	/	0.463
4gdy	0X1	Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial	2.6.1.39	0.462
3e32	ED2	Protein farnesyltransferase subunit beta	2.5.1.58	0.461
3jsi	WTC	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	/	0.461
4fry	NAD	Putative signal-transduction protein with CBS domains	/	0.461
4gdd	NAI	UDP-galactopyranose mutase	/	0.461
4h9t	HL4	Phosphotriesterase	/	0.460
4j53	1J4	Serine/threonine-protein kinase PLK1	2.7.11.21	0.460
4m9a	FDA	Acyl-CoA dehydrogenase	/	0.460
4yj2	GTP	Tubulin alpha-1B chain	/	0.460
1s64	778	Geranylgeranyl transferase type-1 subunit beta	2.5.1.59	0.459
2eix	FAD	NADH-cytochrome b5 reductase	/	0.459
3dyq	PCG	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	/	0.459
4bzb	DGT	Deoxynucleoside triphosphate triphosphohydrolase SAMHD1	3.1.5	0.459
4hfr	14M	Corticosteroid 11-beta-dehydrogenase isozyme 1	1.1.1.146	0.459
3uay	ADN	Purine nucleoside phosphorylase DeoD-type	/	0.458
4gi2	NAP	Crotonyl-CoA carboxylase/reductase	/	0.458
5czy	SAM	Eukaryotic huntingtin interacting protein B	/	0.458
1sa4	JAN	Protein farnesyltransferase subunit beta	2.5.1.58	0.457
1xe6	5FP	Plasmepsin-2	3.4.23.39	0.457
2fw3	BUI	Carnitine O-palmitoyltransferase 2, mitochondrial	2.3.1.21	0.457
2r8p	T6F	Transketolase 1	/	0.457
4bv9	NDP	Ketimine reductase mu-crystallin	1.5.1.25	0.457
1obb	NAD	Alpha-glucosidase	3.2.1.20	0.456
2v7q	ATP	ATP synthase subunit alpha, mitochondrial	/	0.455
2v7q	ATP	ATP synthase subunit beta, mitochondrial	3.6.3.14	0.455
1rne	C60	Renin	3.4.23.15	0.454
1rt9	IMH	Purine nucleoside phosphorylase	2.4.2.1	0.454
2qim	ZEA	Class 10 plant pathogenesis-related protein	/	0.453
2r8o	T5X	Transketolase 1	/	0.453
3bk2	U5P	Ribonuclease J	/	0.453
4e90	7RG	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	/	0.453
4gdc	NDP	UDP-galactopyranose mutase	/	0.453
4hbm	0Y7	E3 ubiquitin-protein ligase Mdm2	6.3.2	0.453
1c9k	5GP	Bifunctional adenosylcobalamin biosynthesis protein CobU	/	0.452
1qyw	5SD	Estradiol 17-beta-dehydrogenase 1	1.1.1.62	0.452
3dy8	5GP	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	/	0.452
1mzc	BNE	Protein farnesyltransferase subunit beta	2.5.1.58	0.451
3gqv	NAP	Enoyl reductase LovC	1	0.451
4nie	NBH	Nuclear receptor ROR-gamma	/	0.451
1xdd	AAY	Integrin alpha-L	/	0.450
2q1s	NAI	Putative nucleotide sugar epimerase/ dehydratase	/	0.450
4gv0	8ME	Poly [ADP-ribose] polymerase 3	2.4.2.30	0.450
5c41	ACP	Ribokinase	/	0.450
2g1o	2IG	Renin	3.4.23.15	0.448
2ifa	FMN	Uncharacterized protein	/	0.448
4bca	FAD	Alkyldihydroxyacetonephosphate synthase, peroxisomal	2.5.1.26	0.448
1rfg	GMP	Purine nucleoside phosphorylase	2.4.2.1	0.447
3bgx	MEF	Thymidylate synthase	/	0.447
3dyl	PCG	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	/	0.447
3elb	C5P	Ethanolamine-phosphate cytidylyltransferase	2.7.7.14	0.447
4gv4	MEJ	Poly [ADP-ribose] polymerase 3	2.4.2.30	0.447
1n83	CLR	Nuclear receptor ROR-alpha	/	0.446
2djx	FMN	Dihydroorotate dehydrogenase (fumarate)	1.3.98.1	0.446
2vig	FAD	Short-chain specific acyl-CoA dehydrogenase, mitochondrial	1.3.8.1	0.446
4bfu	ZVU	Pantothenate kinase	2.7.1.33	0.446
4ddh	MS0	Pantothenate synthetase	6.3.2.1	0.446
4qxa	GTP	Ras-related protein Rab-9A	/	0.446
1tqf	32P	Beta-secretase 1	3.4.23.46	0.445
2bbw	GP5	Adenylate kinase 4, mitochondrial	/	0.445
2zjm	F1M	Beta-secretase 1	3.4.23.46	0.445
3m53	SAH	Histone-lysine N-methyltransferase SETD7	2.1.1.43	0.445
3rpe	FAD	Putative modulator of drug activity	/	0.445
4eb5	PLP	Cysteine desulfurase IscS 2	/	0.445
4g2l	0WL	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	/	0.445
4o7u	THF	Thymidylate synthase	/	0.445
1gco	NAD	Glucose 1-dehydrogenase	1.1.1.47	0.444
1kbo	340	NAD(P)H dehydrogenase [quinone] 1	1.6.5.2	0.444
1n95	FTH	Protein farnesyltransferase subunit beta	2.5.1.58	0.444
1rfv	ADP	Pyridoxal kinase	2.7.1.35	0.444
2a5h	SAM	L-lysine 2,3-aminomutase	5.4.3.2	0.444
2dy9	ADP	Nucleoside diphosphate kinase	2.7.4.6	0.444
2get	COK	Pantothenate kinase	2.7.1.33	0.444
2ohv	NHL	Glutamate racemase	/	0.444
3etd	NDP	Glutamate dehydrogenase 1, mitochondrial	1.4.1.3	0.444
3qtt	ANP	Pantothenate synthetase	/	0.444
3v2u	ATP	Protein GAL3	/	0.444
4bby	FAD	Alkyldihydroxyacetonephosphate synthase, peroxisomal	2.5.1.26	0.444
1xva	SAM	Glycine N-methyltransferase	2.1.1.20	0.443
2c12	FAD	Nitroalkane oxidase	1.7.3.1	0.443
2dxe	GDP	Nucleoside diphosphate kinase	2.7.4.6	0.443
2vet	UMP	Thymidylate synthase	/	0.443
4pzr	COA	Histone acetyltransferase p300	/	0.443
1q0r	AKT	Aclacinomycin methylesterase RdmC	3.1.1.95	0.442
2gv8	NDP	Thiol-specific monooxygenase	1.14.13	0.442
2il2	LIX	Renin	3.4.23.15	0.442
3frk	TQP	QdtB	/	0.442
3zvm	ADP	Bifunctional polynucleotide phosphatase/kinase	2.7.1.78	0.442
4a6r	TA8	Probable aminotransferase	/	0.442
4b63	NAP	L-ornithine N(5)-monooxygenase	/	0.442
4dpt	AGS	Mevalonate diphosphate decarboxylase	/	0.442
3c8b	ARG_ARG_GLY_ILE_NH2	Botulinum neurotoxin type A	3.4.24.69	0.441
3i0p	NAD	Malate dehydrogenase, putative	/	0.441
3u4o	08E	Genome polyprotein	2.7.7.48	0.441
4d03	NAP	Phenylacetone monooxygenase	1.14.13.92	0.441
1q23	FUA	Chloramphenicol acetyltransferase	2.3.1.28	0.440
3k3e	PDB	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	/	0.440
3kji	ADP	CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC	/	0.440
3zbz	OVE	2',3'-cyclic-nucleotide 3'-phosphodiesterase	3.1.4.37	0.440
4b68	NAP	L-ornithine N(5)-monooxygenase	/	0.440
4lzw	THM	Uridine phosphorylase	/	0.440
4r81	FMN	Predicted NADH dehydrogenase	/	0.440