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Receptor
PDB id Resolution Class Description Source Keywords
2YBQ 2 Å EC: 2.1.1.107 THE X-RAY STRUCTURE OF THE SAM-DEPENDENT UROPORPHYRINOGEN II METHYLTRANSFERASE NIRE FROM PSEUDOMONAS AERUGINOSA IN COMPLS AH AND UROPORPHYRINOGEN III PSEUDOMONAS AERUGINOSA TRANSFERASE HEME D1 BIOSYNTHESIS
Ref.: CRYSTAL STRUCTURE OF THE HEME D1 BIOSYNTHESIS ENZYME NIRE IN COMPLEX WITH ITS SUBSTRATE REVEALS NEW INSIGHTS INTO THE CATALYTIC MECHANISM OF S-ADENOSYL-L-METHIONINE-DEPENDENT UROPORPHYRINOGEN III METHYLTRANSFERASES. J.BIOL.CHEM. V. 2
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAH A:1267;
Valid;
none;
submit data
384.411 C14 H20 N6 O5 S c1nc(...
UP2 A:1268;
Valid;
none;
submit data
836.795 C40 H44 N4 O16 C1c2c...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2YBQ 2 Å EC: 2.1.1.107 THE X-RAY STRUCTURE OF THE SAM-DEPENDENT UROPORPHYRINOGEN II METHYLTRANSFERASE NIRE FROM PSEUDOMONAS AERUGINOSA IN COMPLS AH AND UROPORPHYRINOGEN III PSEUDOMONAS AERUGINOSA TRANSFERASE HEME D1 BIOSYNTHESIS
Ref.: CRYSTAL STRUCTURE OF THE HEME D1 BIOSYNTHESIS ENZYME NIRE IN COMPLEX WITH ITS SUBSTRATE REVEALS NEW INSIGHTS INTO THE CATALYTIC MECHANISM OF S-ADENOSYL-L-METHIONINE-DEPENDENT UROPORPHYRINOGEN III METHYLTRANSFERASES. J.BIOL.CHEM. V. 2
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2YBQ - UP2 C40 H44 N4 O16 C1c2c(c(c(....
2 2YBO - SAH C14 H20 N6 O5 S c1nc(c2c(n....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2YBQ - UP2 C40 H44 N4 O16 C1c2c(c(c(....
2 2YBO - SAH C14 H20 N6 O5 S c1nc(c2c(n....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2YBQ - UP2 C40 H44 N4 O16 C1c2c(c(c(....
2 2YBO - SAH C14 H20 N6 O5 S c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SAH; Similar ligands found: 211
No: Ligand ECFP6 Tc MDL keys Tc
1 SAH 1 1
2 5X8 0.759494 0.969697
3 A7D 0.734177 0.926471
4 TT8 0.709302 0.970588
5 DSH 0.692308 0.914286
6 SXZ 0.692308 0.916667
7 DTA 0.666667 0.857143
8 3DH 0.662338 0.869565
9 S8M 0.655556 0.901408
10 SFG 0.635294 0.954545
11 SA8 0.62069 0.915493
12 EEM 0.617977 0.890411
13 MTA 0.615385 0.869565
14 SAI 0.613636 0.955882
15 S7M 0.586957 0.916667
16 36A 0.586538 0.90411
17 K15 0.583333 0.878378
18 ADN 0.573333 0.84058
19 RAB 0.573333 0.84058
20 XYA 0.573333 0.84058
21 62X 0.572917 0.855263
22 5CD 0.571429 0.852941
23 0UM 0.5625 0.876712
24 5N5 0.558442 0.84058
25 A4D 0.551282 0.867647
26 SAM 0.537634 0.916667
27 SMM 0.536842 0.88
28 SSA 0.536842 0.712644
29 KB1 0.534653 0.902778
30 A5D 0.532609 0.857143
31 SIB 0.53125 0.928571
32 EP4 0.530864 0.819444
33 DSZ 0.530612 0.732558
34 GSU 0.53 0.752941
35 A 0.529412 0.763158
36 LMS 0.529412 0.694118
37 AMP 0.529412 0.763158
38 5CA 0.525773 0.712644
39 ME8 0.524752 0.8125
40 M2T 0.52439 0.821918
41 6RE 0.523256 0.824324
42 GJV 0.522727 0.813333
43 AAT 0.515789 0.863014
44 LSS 0.515152 0.696629
45 KAA 0.514852 0.727273
46 J7C 0.511364 0.835616
47 A5A 0.510417 0.697674
48 SON 0.505495 0.805195
49 SRP 0.505155 0.805195
50 F0P 0.504505 0.915493
51 54H 0.5 0.681818
52 VMS 0.5 0.681818
53 ADX 0.5 0.694118
54 CA0 0.5 0.769231
55 AMO 0.5 0.805195
56 5AL 0.5 0.779221
57 KH3 0.5 0.866667
58 NVA LMS 0.49505 0.707865
59 AHX 0.49505 0.753086
60 TSB 0.494949 0.689655
61 53H 0.494949 0.674157
62 G5A 0.494737 0.712644
63 ABM 0.494382 0.74359
64 A2D 0.494382 0.74359
65 ZAS 0.494253 0.808219
66 A6D 0.490196 0.759494
67 8QN 0.49 0.779221
68 GEK 0.49 0.956522
69 GAP 0.489583 0.769231
70 AN2 0.48913 0.734177
71 A3S 0.48913 0.884058
72 S4M 0.488889 0.831169
73 SRA 0.488636 0.746835
74 LAD 0.485437 0.810127
75 52H 0.484848 0.674157
76 A12 0.483516 0.759494
77 BA3 0.483516 0.74359
78 AP2 0.483516 0.759494
79 NEC 0.483146 0.788732
80 AOC 0.483146 0.842857
81 Y3J 0.481481 0.768116
82 VRT 0.479167 0.861111
83 50T 0.478723 0.734177
84 B4P 0.478261 0.74359
85 ADP 0.478261 0.74359
86 5AS 0.478261 0.655556
87 AP5 0.478261 0.74359
88 A3N 0.477778 0.830986
89 YSA 0.476636 0.712644
90 XAH 0.476636 0.768293
91 0XU 0.473684 0.897059
92 AT4 0.473118 0.7375
93 WAQ 0.471154 0.807692
94 NSS 0.470588 0.712644
95 5AD 0.468354 0.791045
96 AU1 0.468085 0.725
97 M33 0.468085 0.734177
98 MAO 0.467391 0.797468
99 TXA 0.466667 0.759494
100 NB8 0.466667 0.775
101 A3G 0.466667 0.871429
102 3AM 0.465909 0.727273
103 DAL AMP 0.465347 0.779221
104 8X1 0.465347 0.707865
105 A3T 0.463158 0.842857
106 ATP 0.463158 0.74359
107 HEJ 0.463158 0.74359
108 ACP 0.463158 0.746835
109 7D7 0.4625 0.785714
110 LEU LMS 0.461538 0.688889
111 9ZA 0.460784 0.740741
112 9ZD 0.460784 0.740741
113 5FA 0.458333 0.74359
114 AQP 0.458333 0.74359
115 AR6 0.458333 0.766234
116 APC 0.458333 0.759494
117 APR 0.458333 0.766234
118 PRX 0.458333 0.746835
119 F2R 0.457627 0.75
120 IOT 0.456897 0.761905
121 4AD 0.456311 0.794872
122 PAJ 0.456311 0.722892
123 WSA 0.45614 0.72093
124 YAP 0.453704 0.794872
125 8PZ 0.453704 0.712644
126 FA5 0.453704 0.805195
127 ADP PO3 0.453608 0.763158
128 ADV 0.453608 0.782051
129 NVA 2AD 0.453608 0.849315
130 SAP 0.453608 0.728395
131 AGS 0.453608 0.728395
132 RBY 0.453608 0.782051
133 AD9 0.453608 0.725
134 PTJ 0.45283 0.731707
135 MHZ 0.452632 0.797468
136 00A 0.451923 0.740741
137 A3P 0.451613 0.74026
138 YLP 0.451327 0.771084
139 7MD 0.45045 0.768293
140 ALF ADP 0.45 0.707317
141 ADP ALF 0.45 0.707317
142 2VA 0.447917 0.819444
143 OOB 0.446602 0.779221
144 ANP 0.444444 0.725
145 T99 0.444444 0.7375
146 ACQ 0.444444 0.746835
147 TAT 0.444444 0.7375
148 P5A 0.443396 0.719101
149 7D5 0.443182 0.708861
150 A1R 0.442308 0.7625
151 YLC 0.439655 0.790123
152 2AM 0.438202 0.717949
153 DLL 0.438095 0.779221
154 ARG AMP 0.4375 0.759036
155 A22 0.436893 0.734177
156 D3Y 0.436893 0.859155
157 ATF 0.435644 0.716049
158 MYR AMP 0.435185 0.746988
159 80F 0.434426 0.75
160 SO8 0.434343 0.808219
161 OAD 0.433962 0.769231
162 3UK 0.433962 0.769231
163 TAD 0.433628 0.765432
164 25A 0.432692 0.74359
165 6YZ 0.431373 0.746835
166 VO4 ADP 0.431373 0.734177
167 ADP VO4 0.431373 0.734177
168 9SN 0.431193 0.731707
169 TYM 0.431034 0.805195
170 B5V 0.429907 0.759494
171 PR8 0.429907 0.8
172 ADQ 0.428571 0.746835
173 YLB 0.42735 0.771084
174 9K8 0.425926 0.67033
175 1ZZ 0.425926 0.746988
176 FYA 0.425926 0.779221
177 3OD 0.425926 0.769231
178 PPS 0.425743 0.674419
179 MAP 0.423077 0.707317
180 A2P 0.421053 0.727273
181 4YB 0.421053 0.735632
182 9X8 0.420561 0.75
183 ADP BMA 0.420561 0.746835
184 TYR AMP 0.419643 0.794872
185 5SV 0.419048 0.731707
186 3NZ 0.416667 0.824324
187 YLA 0.416667 0.771084
188 8Q2 0.415254 0.688889
189 A3R 0.415094 0.7625
190 B5Y 0.414414 0.75
191 B5M 0.414414 0.75
192 48N 0.413793 0.753086
193 LPA AMP 0.413793 0.768293
194 AYB 0.413223 0.761905
195 ACK 0.413043 0.710526
196 QQY 0.413043 0.696203
197 BIS 0.412844 0.719512
198 JB6 0.412844 0.7625
199 PAP 0.41 0.730769
200 DQV 0.408696 0.75641
201 OVE 0.408602 0.7125
202 AMP DBH 0.40708 0.746835
203 4UV 0.40708 0.75
204 3AD 0.406977 0.852941
205 AF3 ADP 3PG 0.40678 0.743902
206 OMR 0.40678 0.738095
207 LAQ 0.405172 0.768293
208 A A 0.40367 0.74359
209 7C5 0.403509 0.789474
210 7MC 0.403361 0.75
211 4UU 0.4 0.75
Ligand no: 2; Ligand: UP2; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 UP2 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2YBQ; Ligand: UP2; Similar sites found with APoc: 99
This union binding pocket(no: 1) in the query (biounit: 2ybq.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
1 2P3V SRT 1.17188
2 2OFD NGA 1.40845
3 2G30 ALA ALA PHE 1.55039
4 1UH4 GLC 1.71233
5 4P7U 1PS 1.78571
6 3RGQ 5P5 1.92308
7 3OII SAH 1.97628
8 3KVY URA 2.05479
9 4MGA 27L 2.35294
10 1YP4 ADP 2.39726
11 5A7Y SAH 2.39726
12 4R29 SAM 2.67857
13 4RF7 ARG 2.73973
14 2C5S AMP 2.73973
15 3A16 PXO 2.73973
16 1KJ1 MAN 2.75229
17 2VDF OCT 2.7668
18 6B2M COA 2.7972
19 4CNE SAH 2.99625
20 3TTZ 07N 3.0303
21 3CBC DBS 3.0303
22 3AKI AH8 3.08219
23 3A23 GAL 3.08219
24 6B5K TYD 3.08219
25 5KJW 53C 3.08219
26 4NZ6 DGL 3.19489
27 4RYV ZEA 3.22581
28 3GYQ SAM 3.30882
29 2WCV FUC 3.57143
30 3CYQ AMU 3.62319
31 4GC1 MAN MAN 3.62319
32 4BS0 6NT 3.76712
33 2QHV OC9 3.80952
34 5CSS G3P 3.9823
35 6EK3 OUL 4.0724
36 4A34 FUL 4.08163
37 5YJS SAL 4.10959
38 5DYO FLU 4.12844
39 4JAL SAH 4.19162
40 2OQ2 A3P 4.21456
41 5VJN ADE 4.27807
42 5VJN IR8 4.27807
43 1I1Q TRP 4.45205
44 3NJQ NJQ 4.66321
45 4IO2 GLU 4.83871
46 4UXU MLK 5.04587
47 5HV7 RBL 5.04587
48 4NOS ITU 5.13699
49 3ESS 18N 5.21739
50 4P86 5GP 5.46448
51 5G48 1FL 5.47945
52 3QDV A2G 5.59441
53 3QDW A2G 5.59441
54 3QDX A2G GAL 5.59441
55 3QDT A2G GAL 5.59441
56 3QDY A2G GAL 5.59441
57 4LED XXR 5.59701
58 4UCF GLA 5.82192
59 5XHA FRU 5.82192
60 5ZZO FLC 5.97015
61 4C25 13P 6.13208
62 5D63 FUC GLA GLA 6.14334
63 5D63 FUC GAL GLA 6.14334
64 4WOE ADP 6.16438
65 1O9P MLA 6.16438
66 4OIT MAN 6.19469
67 4YJK URA 6.34921
68 1WD4 AHR 6.50685
69 2X2T GAL NGA 6.53595
70 3OQJ 3CX 6.61479
71 3NK7 SAM 7.22022
72 5Z21 OXM 7.53425
73 2CI5 HCS 8.09859
74 1RYD GLC 8.21918
75 5H6S HDH 8.21918
76 3D36 ADP 8.69565
77 3SAO DBH 8.75
78 3H0L ADP 8.90411
79 6GNO XDI 9.62963
80 1MXI SAH 10
81 5FUI APY 10.6061
82 3KO0 TFP 10.8911
83 3ZF8 GDP 10.9589
84 5HW4 SAM 11.6935
85 2XG5 EC2 12.1387
86 2XG5 EC5 12.1387
87 5OCG 9R5 12.1693
88 6FA4 D1W 13.8728
89 2VDV SAM 14.2276
90 2YKL NLD 16.2037
91 1WNG SAH 18.4906
92 1VCE SAH 18.4906
93 6GEW SAH 22.2603
94 6GEW SFG 22.2603
95 5N0O SAM 24.3151
96 6MJF SAH 25.3425
97 2E0N SAH 28.1853
98 2QBU SAH 28.8793
99 1CBF SAH 42.8082
Pocket No.: 2; Query (leader) PDB : 2YBQ; Ligand: UP2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2ybq.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2YBQ; Ligand: SAH; Similar sites found with APoc: 104
This union binding pocket(no: 3) in the query (biounit: 2ybq.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 1ZEI CRS None
2 2P3V SRT 1.17188
3 4KBA 1QM 1.36986
4 5W4W 9WG 1.36986
5 2OFD NGA 1.40845
6 2G30 ALA ALA PHE 1.55039
7 1UH4 GLC 1.71233
8 1Q8V MAN MAN MAN 1.98413
9 2PHX MAN MAN MAN MAN 1.98413
10 4ARE FLC 2.05479
11 3RWP ABQ 2.39726
12 5A7Y SAH 2.39726
13 1YP4 ADP 2.39726
14 3JQ7 DX2 2.43056
15 1TL2 NDG 2.54237
16 5WHU SIA 2.68456
17 5WHU SIA GAL GLC 2.68456
18 4RF7 ARG 2.73973
19 2C5S AMP 2.73973
20 3A16 PXO 2.73973
21 2VDF OCT 2.7668
22 3CBC DBS 3.0303
23 3TTZ 07N 3.0303
24 5KJW 53C 3.08219
25 3AKI AH8 3.08219
26 3A23 GAL 3.08219
27 4NZ6 DGL 3.19489
28 4RYV ZEA 3.22581
29 2HYQ MAN MAN 3.27869
30 2GUD MAN 3.27869
31 2GUC MAN 3.27869
32 3GYQ SAM 3.30882
33 1UWK NAD 3.76712
34 1UWK URO 3.76712
35 4BS0 6NT 3.76712
36 2QHV OC9 3.80952
37 6EK3 OUL 4.0724
38 5YJS SAL 4.10959
39 1OUK 084 4.10959
40 5DYO FLU 4.12844
41 4JAL SAH 4.19162
42 1Z6K OAA 4.43686
43 2Z3U CRR 4.45205
44 2XVD AS6 4.45205
45 5YV5 ADP 4.45205
46 3G5D 1N1 4.54545
47 5CIC 51R 4.79452
48 3VRY B43 4.79452
49 4O08 PO6 4.98442
50 5HV7 RBL 5.04587
51 5C9P FUC 5.13699
52 1F9V ADP 5.18732
53 3ESS 18N 5.21739
54 3GD8 GOL 5.38117
55 5G48 1FL 5.47945
56 1GQG DCD 5.47945
57 4CP8 MLI 5.47945
58 4QB6 GCU XYP 5.4878
59 3QDV A2G 5.59441
60 3QDW A2G 5.59441
61 3QDX A2G GAL 5.59441
62 3QDT A2G GAL 5.59441
63 3QDY A2G GAL 5.59441
64 5XHA FRU 5.82192
65 3KDM TES 5.9633
66 5D63 FUC GLA GLA 6.14334
67 5D63 FUC GAL GLA 6.14334
68 4WOE ADP 6.16438
69 1O9P MLA 6.16438
70 2PNC CLU 6.50685
71 1WD4 AHR 6.50685
72 6GH9 MIX 6.50685
73 2X2T GAL NGA 6.53595
74 3OQJ 3CX 6.61479
75 1QD1 FON 7.19178
76 1KNM LAT 7.69231
77 3WXL ADP 7.87671
78 1RYD GLC 8.21918
79 2VGD XYP XYP 8.7156
80 3SAO DBH 8.75
81 3H0L ADP 8.90411
82 1MXI SAH 10
83 2X1E X1E 10.274
84 5FUI APY 10.6061
85 5LXT GTP 10.8647
86 3ZF8 GDP 10.9589
87 5HW4 SAM 11.6935
88 6MVU K4V 11.9863
89 2XG5 EC2 12.1387
90 2XG5 EC5 12.1387
91 5OCG 9R5 12.1693
92 6FA4 D1W 13.8728
93 1YXM ADE 14.3836
94 2YKL NLD 16.2037
95 1WNG SAH 18.4906
96 1VCE SAH 18.4906
97 4USI AKG 21.4286
98 6GEW SAH 22.2603
99 6GEW SFG 22.2603
100 5N0O SAM 24.3151
101 6MJF SAH 25.3425
102 2E0N SAH 28.1853
103 2QBU SAH 28.8793
104 1CBF SAH 42.8082
Pocket No.: 4; Query (leader) PDB : 2YBQ; Ligand: SAH; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2ybq.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
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