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Receptor
PDB id Resolution Class Description Source Keywords
5H5F 1.7 Å EC: 2.1.1.- THE CRYSTAL STRUCTURE OF THE YEAST ARGININE METHYLTRANSFERAS COMPLEXED WITH SAM SACCHAROMYCES CEREVISIAE (STRAIN ATCC S288C) ARGININE METHYLTRANSFERASE SPOUT FOLD TRANSFERASE
Ref.: A FLEXIBLE COFACTOR-BINDING LOOP IN THE NOVEL ARGIN METHYLTRANSFERASE SFM1. FEBS LETT. V. 591 433 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAM A:301;
Valid;
Atoms found LESS than expected: % Diff = 0;
Kd = 37.2 uM
398.437 C15 H22 N6 O5 S C[S@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5H5F 1.7 Å EC: 2.1.1.- THE CRYSTAL STRUCTURE OF THE YEAST ARGININE METHYLTRANSFERAS COMPLEXED WITH SAM SACCHAROMYCES CEREVISIAE (STRAIN ATCC S288C) ARGININE METHYLTRANSFERASE SPOUT FOLD TRANSFERASE
Ref.: A FLEXIBLE COFACTOR-BINDING LOOP IN THE NOVEL ARGIN METHYLTRANSFERASE SFM1. FEBS LETT. V. 591 433 2017
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 60 families.
1 5H5E - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 5H5F Kd = 37.2 uM SAM C15 H22 N6 O5 S C[S@@+](CC....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 54 families.
1 5H5E - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 5H5F Kd = 37.2 uM SAM C15 H22 N6 O5 S C[S@@+](CC....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 47 families.
1 5H5E - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 5H5F Kd = 37.2 uM SAM C15 H22 N6 O5 S C[S@@+](CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SAM; Similar ligands found: 202
No: Ligand ECFP6 Tc MDL keys Tc
1 SAM 1 1
2 SMM 0.792683 0.96
3 S4M 0.6875 0.909091
4 S7M 0.670455 0.945946
5 M2T 0.636364 0.878378
6 GEK 0.612903 0.931507
7 SAI 0.571429 0.878378
8 ADN 0.565789 0.773333
9 RAB 0.565789 0.773333
10 XYA 0.565789 0.773333
11 5CD 0.564103 0.783784
12 EP4 0.5625 0.826667
13 SA8 0.56044 0.945205
14 SFG 0.555556 0.875
15 5X8 0.555556 0.888889
16 5N5 0.551282 0.773333
17 A4D 0.544304 0.797297
18 EEM 0.542553 0.945946
19 SAH 0.537634 0.916667
20 DTA 0.536585 0.789474
21 62X 0.535354 0.884615
22 MTA 0.53012 0.875
23 3DH 0.517647 0.849315
24 5AL 0.510417 0.743902
25 54H 0.510204 0.673913
26 VMS 0.510204 0.673913
27 0UM 0.51 0.857143
28 AMP 0.505747 0.707317
29 LMS 0.505747 0.666667
30 A 0.505747 0.707317
31 ABM 0.505618 0.753086
32 A5A 0.505155 0.688889
33 SON 0.5 0.746988
34 SSA 0.5 0.684783
35 6RE 0.5 0.78481
36 K15 0.5 0.883117
37 5AD 0.5 0.75
38 SRP 0.5 0.746988
39 LSS 0.49505 0.706522
40 CA0 0.494624 0.714286
41 A12 0.494505 0.705882
42 AP2 0.494505 0.705882
43 ME8 0.490385 0.841463
44 TSB 0.49 0.681319
45 53H 0.49 0.666667
46 DAL AMP 0.49 0.765432
47 5CA 0.49 0.684783
48 ACP 0.489362 0.694118
49 ADP 0.48913 0.690476
50 5AS 0.48913 0.648936
51 J7C 0.488889 0.772152
52 A2D 0.488889 0.690476
53 ZAS 0.488636 0.769231
54 9ZD 0.485149 0.729412
55 9ZA 0.485149 0.729412
56 8QN 0.485149 0.743902
57 GAP 0.484536 0.73494
58 AN2 0.483871 0.682353
59 A3S 0.483871 0.813333
60 A7D 0.483871 0.851351
61 GJV 0.483516 0.775
62 SRA 0.483146 0.694118
63 LAD 0.480769 0.752941
64 KAA 0.480769 0.698925
65 GSU 0.480769 0.722222
66 AMO 0.480392 0.746988
67 DSZ 0.480392 0.703297
68 52H 0.48 0.666667
69 M33 0.478723 0.722892
70 BA3 0.478261 0.690476
71 MAO 0.478261 0.82716
72 NEC 0.477778 0.75
73 AOC 0.477778 0.776316
74 DSH 0.477778 0.842105
75 SXZ 0.47619 0.894737
76 AHX 0.475728 0.701149
77 NVA LMS 0.475728 0.736264
78 Y3J 0.47561 0.706667
79 G5A 0.474227 0.684783
80 A3T 0.473684 0.8
81 B4P 0.473118 0.690476
82 AP5 0.473118 0.690476
83 A3N 0.472527 0.766234
84 KB1 0.471698 0.833333
85 PRX 0.46875 0.73494
86 APC 0.46875 0.705882
87 AT4 0.468085 0.686047
88 PAJ 0.466019 0.712644
89 4AD 0.466019 0.759036
90 RBY 0.463918 0.72619
91 ADP PO3 0.463918 0.728395
92 ADV 0.463918 0.72619
93 ADX 0.463158 0.666667
94 MHZ 0.463158 0.82716
95 AU1 0.463158 0.674419
96 YAP 0.462963 0.738095
97 TXA 0.462264 0.72619
98 NB8 0.462264 0.72093
99 A3G 0.461538 0.802632
100 VRT 0.459184 0.842105
101 XAH 0.458716 0.715909
102 YSA 0.458716 0.684783
103 HEJ 0.458333 0.690476
104 50T 0.458333 0.682353
105 ATP 0.458333 0.690476
106 LEU LMS 0.457143 0.717391
107 7D7 0.45679 0.723684
108 KH3 0.455357 0.871795
109 ACQ 0.454545 0.694118
110 AR6 0.453608 0.710843
111 APR 0.453608 0.710843
112 AQP 0.453608 0.690476
113 5FA 0.453608 0.690476
114 NSS 0.451923 0.703297
115 FA5 0.449541 0.746988
116 A5D 0.44898 0.789474
117 AD9 0.44898 0.674419
118 AGS 0.44898 0.678161
119 SAP 0.44898 0.678161
120 PTJ 0.448598 0.72093
121 YLB 0.448276 0.758621
122 YLP 0.447368 0.738636
123 8X1 0.446602 0.680851
124 D3Y 0.446602 0.792208
125 ADP ALF 0.445545 0.678161
126 ALF ADP 0.445545 0.678161
127 3AM 0.444444 0.674699
128 MYR AMP 0.444444 0.776471
129 OAD 0.443396 0.73494
130 2VA 0.443299 0.779221
131 S8M 0.442308 0.831169
132 OOB 0.442308 0.722892
133 TYR AMP 0.441441 0.759036
134 6YZ 0.441176 0.694118
135 ADP VO4 0.441176 0.702381
136 VO4 ADP 0.441176 0.702381
137 T99 0.44 0.686047
138 TAT 0.44 0.686047
139 ANP 0.44 0.674419
140 WAQ 0.439252 0.75
141 B5Y 0.436364 0.717647
142 8PZ 0.436364 0.684783
143 F0P 0.435897 0.844156
144 YLC 0.435897 0.755814
145 AAT 0.435644 0.797468
146 1ZZ 0.435185 0.755814
147 9K8 0.435185 0.663158
148 3OD 0.435185 0.73494
149 NVA 2AD 0.434343 0.855263
150 00A 0.433962 0.689655
151 DLL 0.433962 0.722892
152 ARG AMP 0.433628 0.727273
153 7MD 0.433628 0.715909
154 ATF 0.431373 0.666667
155 SO8 0.43 0.792208
156 3UK 0.429907 0.714286
157 A6D 0.429907 0.72619
158 9X8 0.429907 0.717647
159 F2R 0.429752 0.7
160 5SV 0.428571 0.741176
161 AMP DBH 0.428571 0.714286
162 TYM 0.42735 0.746988
163 WSA 0.42735 0.692308
164 9SN 0.427273 0.681818
165 AHZ 0.426087 0.755814
166 P5A 0.425926 0.691489
167 B5V 0.425926 0.705882
168 PR8 0.425926 0.744186
169 A A 0.425926 0.710843
170 3NZ 0.425926 0.807692
171 A1R 0.424528 0.709302
172 2A5 0.424242 0.674419
173 7MC 0.423729 0.719101
174 B5M 0.423423 0.717647
175 7D5 0.422222 0.658824
176 JB6 0.422018 0.709302
177 FYA 0.422018 0.722892
178 AYB 0.421488 0.75
179 A22 0.419048 0.682353
180 MAP 0.419048 0.659091
181 2AM 0.417582 0.666667
182 TAD 0.417391 0.712644
183 A3P 0.416667 0.686747
184 ADP BMA 0.416667 0.714286
185 25A 0.415094 0.690476
186 YLA 0.413223 0.719101
187 8Q2 0.411765 0.663158
188 A3R 0.411215 0.709302
189 ADQ 0.411215 0.694118
190 48N 0.410256 0.72093
191 0XU 0.41 0.824324
192 GA7 0.408696 0.72619
193 7D3 0.40625 0.643678
194 PAP 0.405941 0.678571
195 DQV 0.405172 0.702381
196 OVE 0.404255 0.662791
197 4UV 0.403509 0.697674
198 AF3 ADP 3PG 0.403361 0.712644
199 3AD 0.402299 0.783784
200 CMP 0.402062 0.691358
201 2BA 0.402062 0.682927
202 7C5 0.4 0.731707
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5H5F; Ligand: SAM; Similar sites found with APoc: 148
This union binding pocket(no: 1) in the query (biounit: 5h5f.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 2BOS GLA GAL GLC None
2 2BOS GLA GAL GLC NBU None
3 3OII SAH 1.7094
4 2PZ8 APC 1.7094
5 3HQP FDP 1.7094
6 3O7J 2AL 2.1164
7 1JGT APC 2.13675
8 1O9U ADZ 2.13675
9 3LDW IPE 2.13675
10 1XNG ATP 2.13675
11 1VKJ A3P 2.13675
12 1K7T NAG GAL 2.15054
13 2Q37 3AL 2.20994
14 3GD8 GOL 2.24215
15 4A6F SEP 2.5
16 3GYQ SAM 2.5641
17 3RK1 ATP 2.5641
18 5GZ9 MAN 2.5641
19 3QDV NDG 2.7972
20 4UBS DIF 2.99145
21 3FJG 3PG 2.99145
22 3SZB I1E 2.99145
23 2HXW FLC 2.99145
24 4N14 WR7 2.99145
25 4I9A NCN 3.125
26 5F6U 5VK 3.18471
27 4MUS LY0 3.31754
28 4MUS 2D8 3.31754
29 2DTJ THR 3.37079
30 4JWH SAH 3.4188
31 1KOR ARG 3.4188
32 1KOR ANP 3.4188
33 2WSI FAD 3.4188
34 1YVZ JPC 3.4188
35 1KOR SIN 3.4188
36 4GPS CIT 3.4188
37 5J5Z FAD 3.4188
38 1GRN AF3 3.44828
39 1V2X SAM 3.60825
40 1LNX URI 3.7037
41 3BP1 GUN 3.84615
42 4MCC 21X 3.84615
43 3VOZ 04A 3.84615
44 1Q19 APC 3.84615
45 6BOX SAH 3.84615
46 3FIU AMP 4.2735
47 5CGE 51F 4.2735
48 4XJ7 ADN 4.2735
49 1OAA OAA 4.2735
50 1USR SIA WIA 4.2735
51 2PNC CLU 4.2735
52 1O94 AMP 4.2735
53 3BBD SAH 4.39024
54 4CNE SAH 4.70085
55 1T9D P22 4.70085
56 2Z4T C5P 4.70085
57 5Z2F PDC 4.70085
58 6B2M COA 4.70085
59 5WKC TP9 4.70085
60 3KIF GDL 4.71698
61 5L2R MLA 4.96689
62 2UVO NDG 5.26316
63 4AML GYU 5.26316
64 1OSS BEN 5.38117
65 4JAL SAH 5.38922
66 2C5S AMP 5.55556
67 3G6K FAD 5.55556
68 3G6K POP 5.55556
69 2VN9 GVD 5.55556
70 4BCQ TJF 5.55556
71 3OID TCL 5.55556
72 5O96 SAM 5.71429
73 1XVB BHL BHL 5.88235
74 2YP6 C6W 5.94595
75 3AIA SAM 5.98291
76 1EFV AMP 5.98291
77 1EFV FAD 5.98291
78 3AB4 THR 5.98291
79 2JFV FLC 5.98291
80 5AHW CMP 6.12245
81 3DCM SAM 6.25
82 5TSH ADP 6.41026
83 5V49 MET 6.41026
84 3HGM ATP 6.80272
85 2X7I CIT 6.81818
86 3SBZ MLI 6.83761
87 2YY8 SAM 6.96517
88 2YY8 MTA 6.96517
89 4Y8D 49J 7.14286
90 6EKZ SNP 7.26496
91 1GPM AMP 7.26496
92 3GDN MXN 7.26496
93 2XCU C5P 7.26496
94 3AI3 SOE 7.26496
95 5OFW 9TW 7.62332
96 5GVR LMR 7.69231
97 6FTB M0E 7.69231
98 3BBH SFG 7.80488
99 5FII PHE 7.84314
100 1P9P SAH 8.11966
101 3DLG GWE 8.11966
102 2AWN ADP 8.11966
103 2GEK GDP 8.37438
104 3O7B SAH 8.54701
105 5D9G GLU ASN LEU TYR PHE GLN 8.54701
106 1MJH ATP 8.64198
107 3FO2 BZH 8.6758
108 4NBI D3Y 9.14634
109 6GMR F4K 9.20245
110 5A7Y SAH 9.40171
111 1T36 ORN 9.40171
112 4L2I NAD 9.40171
113 4JWJ SAH 9.40594
114 1CT9 AMP 9.82906
115 4C2C ALA ALA ALA 9.82906
116 1O6B ADP 9.82906
117 2W5P CL8 10.0671
118 1DKU AP2 10.2564
119 2BMB PMM 10.2564
120 2CFM AMP 10.2564
121 5Y4R C2E 10.3448
122 6MJ7 ARG 10.9091
123 2OG2 MLI 11.1111
124 3PTG 932 11.1111
125 3B9Q MLI 11.1111
126 3B99 U51 11.1111
127 1F6D UDP 11.5385
128 4RRG A3T 12.0567
129 5APG EEM 12.973
130 1ZEI CRS 13.2075
131 2Z49 AMG 13.2479
132 2Z3U CRR 13.2479
133 2Z48 A2G 13.2479
134 5TWJ SAM 13.5802
135 2WD7 VGD 14.1026
136 4XH0 ADP 14.1026
137 4JWF SAH 15.2074
138 3H9R TAK 15.5963
139 2WEL K88 16
140 6EMU SAM 16.2393
141 3M2W L8I 16.2393
142 4C2W ANP 17.3077
143 3OKA GDD 19.0476
144 4M00 SUC 23.9316
145 1SQL GUN 26.0274
146 2XG5 EC2 27.0642
147 2XG5 EC5 27.0642
148 4CNG SAH 29.0598
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