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Receptor
PDB id Resolution Class Description Source Keywords
4M3P 1.9 Å EC: 2.1.1.5 BETAINE-HOMOCYSTEINE S-METHYLTRANSFERASE FROM HOMO SAPIENS C WITH HOMOCYSTEINE HOMO SAPIENS ALPHA AND BETA PROTEINS (A/B) TIM BETA/ALPHA-BARREL METHYLTRANSFERASE ACTIVITY HOMOCYSTEINE S-METHYLTRANSFERASACTIVITY TRANSFERASE ACTIVITY METAL ION BINDING BETAINE-HOMOCYSTEINE S-METHYLTRANSFERASE ACTIVITY PROTEIN COMPLEX BETAINE HOMOCYSTEINE TRANSFERASE
Ref.: SPECIFIC POTASSIUM ION INTERACTIONS FACILITATE HOMO BINDING TO BETAINE-HOMOCYSTEINE S-METHYLTRANSFERASE PROTEINS V. 82 2552 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
K B:503;
A:702;
D:503;
C:502;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
39.098 K [K+]
SRT B:501;
D:501;
Invalid;
Invalid;
none;
none;
submit data
150.087 C4 H6 O6 [C@H]...
ZN B:502;
D:502;
A:701;
C:501;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
HCS D:504;
C:503;
B:504;
A:703;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
135.185 C4 H9 N O2 S C(CS)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4M3P 1.9 Å EC: 2.1.1.5 BETAINE-HOMOCYSTEINE S-METHYLTRANSFERASE FROM HOMO SAPIENS C WITH HOMOCYSTEINE HOMO SAPIENS ALPHA AND BETA PROTEINS (A/B) TIM BETA/ALPHA-BARREL METHYLTRANSFERASE ACTIVITY HOMOCYSTEINE S-METHYLTRANSFERASACTIVITY TRANSFERASE ACTIVITY METAL ION BINDING BETAINE-HOMOCYSTEINE S-METHYLTRANSFERASE ACTIVITY PROTEIN COMPLEX BETAINE HOMOCYSTEINE TRANSFERASE
Ref.: SPECIFIC POTASSIUM ION INTERACTIONS FACILITATE HOMO BINDING TO BETAINE-HOMOCYSTEINE S-METHYLTRANSFERASE PROTEINS V. 82 2552 2014
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1LT8 - CIT C6 H8 O7 C(C(=O)O)C....
2 4M3P - HCS C4 H9 N O2 S C(CS)[C@@H....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1LT8 - CIT C6 H8 O7 C(C(=O)O)C....
2 4M3P - HCS C4 H9 N O2 S C(CS)[C@@H....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1LT8 - CIT C6 H8 O7 C(C(=O)O)C....
2 4M3P - HCS C4 H9 N O2 S C(CS)[C@@H....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: HCS; Similar ligands found: 46
No: Ligand ECFP6 Tc MDL keys Tc
1 HCS 1 1
2 DCY 0.608696 0.916667
3 CYS 0.608696 0.916667
4 DAB 0.56 0.851852
5 HSE 0.56 0.821429
6 GGL 0.555556 0.714286
7 DGL 0.555556 0.714286
8 GLU 0.555556 0.714286
9 NVA 0.538462 0.740741
10 API 0.538462 0.689655
11 DBB 0.5 0.692308
12 2RA 0.5 0.75
13 GLN 0.5 0.645161
14 ABA 0.5 0.692308
15 DSN 0.5 0.777778
16 DGN 0.5 0.645161
17 SER 0.5 0.777778
18 ORN 0.482759 0.814815
19 C2N 0.48 0.730769
20 ONL 0.466667 0.645161
21 NLE 0.466667 0.689655
22 CSS 0.464286 0.75
23 DAS 0.461538 0.655172
24 ASP 0.461538 0.655172
25 MSE 0.451613 0.65625
26 UN1 0.451613 0.689655
27 MET 0.451613 0.733333
28 11C 0.451613 0.689655
29 MED 0.451613 0.733333
30 DLY 0.451613 0.785714
31 LYS 0.4375 0.758621
32 DHH 0.4375 0.666667
33 CSO 0.428571 0.636364
34 AS2 0.428571 0.642857
35 LEU 0.428571 0.642857
36 KKA 0.428571 0.685714
37 ONH 0.424242 0.611111
38 NPI 0.424242 0.666667
39 6CL 0.411765 0.666667
40 2FM 0.411765 0.758621
41 26P 0.411765 0.625
42 VUR 0.410256 0.657143
43 3GC 0.410256 0.705882
44 HL5 0.40625 0.75
45 CIR 0.4 0.611111
46 MF3 0.4 0.733333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4M3P; Ligand: HCS; Similar sites found with APoc: 268
This union binding pocket(no: 1) in the query (biounit: 4m3p.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 1U1J MET 1.23153
2 2F5Z FAD 1.47783
3 4MAF ADX 1.48515
4 3KRB NAP 1.49701
5 2YVK MRU 1.60428
6 6CD1 PLS 1.72414
7 5UCD NAP 1.72414
8 4NZN ANP 1.81818
9 4NZN 2OU 1.81818
10 3KJD 78P 1.90217
11 4KWD JF2 1.91083
12 5EP2 AZU 1.95312
13 1YNH SUO 1.97044
14 6ER9 FAD 1.97044
15 5MBX SP5 1.97044
16 5MBX FAD 1.97044
17 1TUF AZ1 1.97044
18 5EB4 FAD 1.97044
19 1FP2 HMO 1.98864
20 3OF1 CMP 2.03252
21 1UCD U5P 2.10526
22 1UCD URA 2.10526
23 3O5X JZG 2.17391
24 2FWP ICR 2.18579
25 3LOO B4P 2.19178
26 2J4K U5P 2.21239
27 5O5Y GLC 2.21675
28 5YB7 ORN 2.21675
29 1YP4 ADP 2.21675
30 6F97 FAD 2.21675
31 5YB7 FAD 2.21675
32 5G09 6DF 2.21675
33 2EXX NAP 2.28758
34 2BEK ATP 2.33463
35 4QM7 GTP 2.33918
36 3OII SAH 2.37154
37 5W4W 9WG 2.41692
38 5HW4 SAM 2.41935
39 2QRY TPS 2.42424
40 1IM8 SAI 2.45902
41 2IHK CSF 2.50627
42 4I4Z 2NE 2.54545
43 3GBR PRP 2.6087
44 5FAH 5VT 2.67857
45 4FWE FAD 2.70936
46 3NJ4 NAD 2.70936
47 5WP5 SAH 2.70936
48 2IVD FAD 2.70936
49 5G3U ITW 2.70936
50 4AOA IK2 2.70936
51 2XVF FAD 2.70936
52 4ZLU ADP 2.70936
53 1H5T DAU 2.73038
54 6AM8 PLT 2.77778
55 6AMI TRP 2.77778
56 2RDE C2E 2.78884
57 6MPT C30 2.7972
58 1U1I NAD 2.80612
59 4HZD COA 2.83688
60 4Y30 SAH 2.849
61 1FA2 DOM 2.95567
62 4JAL SAH 2.99401
63 4AVB CMP 3.003
64 4B6C B5U 3.06122
65 1EBF NAD 3.07263
66 3KYG 5GP 5GP 3.0837
67 2I6A 5I5 3.18841
68 6C2Z P1T 3.2
69 5ZKC 3C0 3.20197
70 4E1O PLP PVH 3.20197
71 5GSN FAD 3.20197
72 5GSN NAP 3.20197
73 5GSN MMZ 3.20197
74 1CT9 GLN 3.20197
75 4JB1 FAD 3.23529
76 4JB1 NAP 3.23529
77 5KVA SAM 3.23741
78 4C5N PXL 3.26087
79 5VJE GOS 3.35196
80 5OJL TXP 3.3557
81 4FOJ C2E 3.40909
82 5OCM NAP 3.43643
83 3LN0 52B 3.44828
84 5MW8 ATP 3.44828
85 2HKJ RDC 3.44828
86 1NJJ ORX 3.44828
87 1Q6D GLC GLC 3.44828
88 5WP4 PC 3.44828
89 5I3B HQE 3.48432
90 2PHN GDP 3.54331
91 4FN4 NAD 3.54331
92 3KVY URA 3.55987
93 4X7G NAP 3.58566
94 2ZJ1 NAD 3.69458
95 2ZJ1 ARJ 3.69458
96 2C0U FAD NBT 3.69458
97 3GAY P6T 3.71517
98 4R5M 4NO 3.7234
99 2O4J VD4 3.76712
100 4A22 TD4 3.77907
101 5FM0 WAQ 3.84615
102 5XK9 DMA 3.87931
103 5XK9 GST 3.87931
104 4XB2 HSE 3.8806
105 4XB2 NDP 3.8806
106 1NE6 SP1 3.88693
107 4CNG SAH 3.92157
108 4WZ8 3W7 3.94089
109 3NKS FAD 3.94089
110 2Q4H AMP 3.9886
111 3HDY FAD 4.03023
112 3HDY GDU 4.03023
113 2XCF BBQ 4.0404
114 1OYF MHN 4.13223
115 5X2N ALA 4.14747
116 6F3M NAD 4.18719
117 5A1S FLC 4.18719
118 4WXG 2BO 4.18719
119 4C3Y FAD 4.18719
120 4B7S QLE 4.18719
121 6FDF SAH 4.19162
122 1NV8 SAM 4.22535
123 1NV8 MEQ 4.22535
124 3HB5 E2B 4.28135
125 3B0P FMN 4.28571
126 1N2X SAM 4.31894
127 3I6I NDP 4.33526
128 4EWN 0VR 4.34783
129 2BLE 5GP 4.35967
130 5TWB FAD 4.36047
131 5ZEC NAP 4.38596
132 4YKG FAD 4.4335
133 1TMX BEZ 4.43686
134 4TO8 FLC 4.45205
135 2CJF RP4 4.4586
136 4PSB GA3 4.51613
137 2C6Q IMP 4.5584
138 1V9A SAH 4.60251
139 5B3A 0JO 4.62725
140 2V5X V5X 4.63918
141 3N8K D1X 4.65116
142 1DFO PLG 4.6798
143 4AF0 IMP 4.6798
144 3WLE NAD 4.69208
145 3C56 PH4 4.88599
146 3N9R TD3 4.88599
147 5ECP ATP 4.93274
148 5K8C NAD 5.02793
149 5AVF TAU 5.05837
150 4FOU C2E 5.12821
151 4C2C ALA VAL PRO ALA 5.17241
152 4PU5 ANP 5.17241
153 3RDO BTN 5.22876
154 1G55 SAH 5.24781
155 4IXH IMP 5.26316
156 5Z2L NDP 5.30612
157 4B7X NAP 5.35714
158 5TUZ SAM 5.36398
159 5TUZ 7L6 5.36398
160 4RPO T6C 5.38117
161 4MDH NAD 5.38922
162 1LYB IVA VAL VAL STA ALA STA 5.39419
163 5MDH NAD 5.40541
164 6CUZ FEV 5.41237
165 1E6E FAD 5.46875
166 1JXZ BCA 5.57621
167 1NZY BCA 5.57621
168 4ZV1 ARG 5.5794
169 3MD0 GDP 5.6338
170 5X8G S0N 5.66502
171 2GVC FAD 5.66502
172 1U1W 3HA 5.7047
173 4GE6 B26 5.73248
174 5OYA CAP 5.7554
175 3KO8 NAD 5.76923
176 1T8U A3P 5.88235
177 5M8T 0TR 5.91133
178 5W5R PYR 5.91133
179 5TBS ADE 5.92335
180 4QTU SAM 5.92593
181 4I42 1HA 5.96491
182 4KQP GLN 6.03448
183 5LNE A2G GAL 6.09756
184 1LLU NAD 6.14035
185 3GDH SAH 6.22407
186 5ODQ 9SB 6.35452
187 1JE1 GMP 6.35593
188 1USI PHE 6.35838
189 4YLG GDP 6.35838
190 3W68 VIV 6.39098
191 4Z0G 5GP 6.40394
192 4Z87 5GP 6.40394
193 5IKR ID8 6.40394
194 3LL5 IPE 6.4257
195 3LL5 ADP 6.4257
196 3LL5 ATP 6.4257
197 1R5L VIV 6.48855
198 2NSJ C2R 6.50888
199 4CQM NAP 6.51341
200 6E2B PT7 6.57895
201 1R37 NAD 6.62824
202 1KY8 NAP 6.65025
203 5TS5 FAD 6.65025
204 1S16 ANP 6.66667
205 2DPM SAM 6.69014
206 3GZ8 APR 6.79012
207 3X0V FAD 6.89655
208 3WOL VAL TYR 6.89655
209 3OND ADN 6.89655
210 3OND NAD 6.89655
211 5BRE 4UZ 6.89655
212 3PT9 SAH 7.14286
213 3PNA CMP 7.14286
214 3QV1 NAD 7.31707
215 1E5Q NDP 7.38916
216 3OVR 5SP 7.45614
217 4JEM C5P 7.64706
218 3C3N FMN 7.69231
219 5J1S ATP 7.74648
220 1H7F C5P 7.7551
221 5GJO PLP 7.86802
222 5H81 NAP 7.96915
223 5XKT GNP 8
224 1Q20 A3P 8.02676
225 1Q20 PLO 8.02676
226 2HMT NAI 8.33333
227 6MVU K4V 8.37438
228 1N2A GTS 8.45771
229 1SG4 CO8 8.46154
230 5MZY 8EZ 8.46774
231 4R74 F6P 8.72274
232 1F8Y 5MD 8.9172
233 6CGD GNP 9.18033
234 6CGD AKN 9.18033
235 5TCI 79V 9.42029
236 1XTP SAI 9.44882
237 1IWE IMP 9.60591
238 4TXJ THM 9.7973
239 6FCX SAH 9.85222
240 5GUD 2IT 9.85222
241 5GUD NDP 9.85222
242 3C3Y SAH 10.1266
243 3KCC CMP 10.3846
244 1TDF FAD 10.7595
245 1TDF NAP 10.7595
246 3PJU C2E 10.8434
247 3GDN FAD 11.0837
248 3GDN HBX 11.0837
249 4ZXA H8N 11.9048
250 4EKV BTN 11.9497
251 4YRY FAD 11.9565
252 1D6S MET PLP 12.4224
253 1D6S PLP MET 12.4224
254 2I8T GDD 12.5749
255 5W97 CHD 12.7753
256 5ZCO CHD 12.7753
257 3RG9 NDP 12.9167
258 3RG9 WRA 12.9167
259 4MS4 2C0 13.0542
260 2DSA HPX 14.2857
261 2DSA GSH 14.2857
262 5EIN NAP 14.8148
263 3NCQ ATP 20.1681
264 5WGG SAM 23.8095
265 5DMM HCS 25.4839
266 5TWJ SAM 26.5432
267 1Q8A HCS 31.5271
268 3BOF HCS 31.7734
Pocket No.: 2; Query (leader) PDB : 4M3P; Ligand: HCS; Similar sites found with APoc: 34
This union binding pocket(no: 2) in the query (biounit: 4m3p.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 1CSI CMX 1.23153
2 1CSI OAA 1.23153
3 2XGT NSS 1.72414
4 3G2O SAM 2.00669
5 2GKS ADP 2.46305
6 1JS3 PLP 142 2.46305
7 1IIM TTP 2.73973
8 2EIX FAD 2.88066
9 5E72 SAM 3.46821
10 3L9W AMP 3.69458
11 5BVA FAD 3.69458
12 3MAX LLX 3.81471
13 2NYA MGD 3.94089
14 2C6Q NDP 4.5584
15 2YVJ NAI 4.58716
16 1PVN MZP 5.05319
17 4QIJ 1HA 5.08982
18 1V47 ADX 5.44413
19 5HV0 AKG 5.52995
20 2AX9 BHM 5.85938
21 5T9F TYR 5.90406
22 5T9F NAP 5.90406
23 5JCA NDP 6.33803
24 5JCA FAD 6.33803
25 2QBU SAH 6.46552
26 4ZOH MCN 6.54762
27 6A8H AHR AHR AHR 7.47664
28 2BP1 NDP 7.77778
29 5WHU SIA 8.05369
30 5WHU SIA GAL GLC 8.05369
31 3DMH SAM 8.13648
32 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 9.47368
33 2GAG NAD 10.0985
34 1N9G NAP 10.3627
Pocket No.: 3; Query (leader) PDB : 4M3P; Ligand: HCS; Similar sites found with APoc: 99
This union binding pocket(no: 3) in the query (biounit: 4m3p.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 2E1A MSE None
2 1RP0 AHZ 1.05634
3 3MKH FAD 1.47783
4 1DAR GDP 1.72414
5 5H7K GDP 1.76322
6 4NMC 2OP 1.97044
7 3B1Q NOS 1.97044
8 5AHM IMP 2
9 3MPI FAD 2.01511
10 5GLN XYS 2.03488
11 2ZMF CMP 2.1164
12 2NVA PL2 2.15054
13 4H4D 10E 2.16718
14 6ECU SAH 2.21519
15 5LRT ADP 2.21675
16 4CYI ATP 2.21675
17 3ZEI AWH 2.25806
18 1U3U NAD 2.40642
19 1U3U BNF 2.40642
20 5T2U NAP 2.41935
21 3PFD FDA 2.54453
22 1G2O IMH 2.61194
23 3QKT ANP 2.65487
24 4GA6 AMP 2.70936
25 3MDV CL6 2.70936
26 5VKT NAP 2.76243
27 1XS5 MET 2.90456
28 1DMR PGD 2.95567
29 2RGO FAD 2.95567
30 1EU1 MGD 2.95567
31 1X54 4AD 3.20197
32 3OU2 SAH 3.21101
33 4C5N ACP 3.26087
34 1Q9I TEO 3.44828
35 1Q9I FAD 3.44828
36 5WP4 SAH 3.44828
37 3EYA FAD 3.44828
38 2A8Y MTA 3.7037
39 1ELU CSS 3.84615
40 5U8U FAD 3.94089
41 3CV3 UDP 3.94089
42 5GM5 CBI 4.09091
43 2QV7 ADP 4.1543
44 6F3N NAD 4.18719
45 3TWO NDP 4.31034
46 3WCA FPS 4.38356
47 5JWI ARG GLU 4.4335
48 1I8T FAD 4.90463
49 4O8A FAD 4.92611
50 5G10 6DK 5.01319
51 1KK1 GNP 5.17241
52 3N17 NAG NAG 5.40541
53 4IQY AR6 5.41667
54 2HSA FMN 5.47264
55 2XB8 XNW 5.47945
56 5NMX FAD 5.66502
57 1VQW FAD 5.66502
58 1EP2 FMN 5.74713
59 3TK1 GDP 5.75758
60 4G5G GDP 5.83756
61 1T8U UAP SGN IDS SGN 5.88235
62 1Z4O GL1 5.88235
63 6CC0 EWM 5.90717
64 4ZUL UN1 6.15764
65 1OLS TDP 6.25
66 4P6X HCY 6.27451
67 1ZOA 140 6.40394
68 2CVQ NDP 6.42202
69 3RNM FAD 6.89655
70 2GJ8 ALF GDP 6.97674
71 4L1F FAD 7.04961
72 2BJU IH4 7.14286
73 5KJZ PCG 7.33333
74 2Q3O FMN 7.41688
75 2XVM SAH 7.53769
76 4IWN GEK 7.86026
77 1Q5D EPB 7.88177
78 4EKQ NPO 8.02139
79 3MJY IJZ 8.09249
80 3MJY FMN 8.09249
81 1WP4 NDP 8.3045
82 3VC3 C6P 8.43023
83 1L3I SAH 8.85417
84 2AG5 NAD 8.94309
85 4PIV NDP 9.1133
86 2C94 TSF 9.375
87 5D85 FLC 9.5092
88 5M58 SAH 10
89 1V7C HEY 10.2564
90 5UIU 8CG 10.5263
91 5NWD 9C8 10.9948
92 4UYE 9F9 11.0169
93 5G4J EXT 11.0837
94 4N02 FNR 11.2045
95 2C49 ADN 11.5894
96 3BQ5 HCS 11.8227
97 4K6B GLU 12.4224
98 2F01 BTQ 14.9606
99 2F01 BTN 14.9606
Pocket No.: 4; Query (leader) PDB : 4M3P; Ligand: HCS; Similar sites found with APoc: 7
This union binding pocket(no: 4) in the query (biounit: 4m3p.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 2E9L OLA 2.46305
2 2E9L PLM 2.46305
3 2E9L BGC 2.46305
4 5LNQ CAA 3.20197
5 4MIG G3F 3.20197
6 3G5N PB2 3.94089
7 5WKC FAD 7.88177
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