Receptor
PDB id Resolution Class Description Source Keywords
3I53 2.08 Å EC: 2.1.1.- CRYSTAL STRUCTURE OF AN O-METHYLTRANSFERASE (NCSB1) FROM NEOCARZINOSTATIN BIOSYNTHESIS IN COMPLEX WITH S-ADENOSYL-L-H OMOCYSTEINE (SAH) STREPTOMYCES CARZINOSTATICUS SUBSP. NEOCARZINOSTATICUS CO-COMPLEX ROSSMANN-LIKE FOLD METHYLTRANSFERASE TRANSFERA
Ref.: MOLECULAR BASIS OF SUBSTRATE PROMISCUITY FOR THE SAM-DEPENDENT O-METHYLTRANSFERASE NCSB1, INVOLVED I BIOSYNTHESIS OF THE ENEDIYNE ANTITUMOR ANTIBIOTIC NEOCARZINOSTATIN. BIOCHEMISTRY V. 48 9590 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL B:402;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
SAH A:401;
B:401;
Valid;
Valid;
none;
none;
submit data
384.411 C14 H20 N6 O5 S c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3I53 2.08 Å EC: 2.1.1.- CRYSTAL STRUCTURE OF AN O-METHYLTRANSFERASE (NCSB1) FROM NEOCARZINOSTATIN BIOSYNTHESIS IN COMPLEX WITH S-ADENOSYL-L-H OMOCYSTEINE (SAH) STREPTOMYCES CARZINOSTATICUS SUBSP. NEOCARZINOSTATICUS CO-COMPLEX ROSSMANN-LIKE FOLD METHYLTRANSFERASE TRANSFERA
Ref.: MOLECULAR BASIS OF SUBSTRATE PROMISCUITY FOR THE SAM-DEPENDENT O-METHYLTRANSFERASE NCSB1, INVOLVED I BIOSYNTHESIS OF THE ENEDIYNE ANTITUMOR ANTIBIOTIC NEOCARZINOSTATIN. BIOCHEMISTRY V. 48 9590 2009
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 57 families.
1 3I53 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 50 families.
1 3I53 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 44 families.
1 1TW2 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 5EEH - P9P C6 H4 Cl N O3 c1cc(c(cc1....
3 5EEG - S8M C14 H20 N10 O3 S c1nc(c2c(n....
4 1TW3 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
5 4WXH - SAH C14 H20 N6 O5 S c1nc(c2c(n....
6 3I53 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
7 1R00 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
8 1QZZ - SAM C15 H22 N6 O5 S C[S@@+](CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SAH; Similar ligands found: 197
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 SXZ 0.692308 0.916667
6 DSH 0.692308 0.914286
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 RAB 0.573333 0.84058
19 ADN 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 SSA 0.536842 0.712644
28 SMM 0.536842 0.88
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 AMP 0.529412 0.763158
36 A 0.529412 0.763158
37 5CA 0.525773 0.712644
38 ME8 0.524752 0.8125
39 M2T 0.52439 0.821918
40 6RE 0.523256 0.824324
41 GJV 0.522727 0.813333
42 AAT 0.515789 0.863014
43 LSS 0.515152 0.696629
44 KAA 0.514852 0.727273
45 J7C 0.511364 0.835616
46 A5A 0.510417 0.697674
47 SON 0.505495 0.805195
48 SRP 0.505155 0.805195
49 5AL 0.5 0.779221
50 VMS 0.5 0.681818
51 KH3 0.5 0.866667
52 ADX 0.5 0.694118
53 CA0 0.5 0.769231
54 AMP MG 0.5 0.74359
55 AMO 0.5 0.805195
56 54H 0.5 0.681818
57 AHX 0.49505 0.753086
58 TSB 0.494949 0.689655
59 53H 0.494949 0.674157
60 G5A 0.494737 0.712644
61 A2D 0.494382 0.74359
62 ABM 0.494382 0.74359
63 ZAS 0.494253 0.808219
64 A6D 0.490196 0.759494
65 8QN 0.49 0.779221
66 GEK 0.49 0.956522
67 GAP 0.489583 0.769231
68 A3S 0.48913 0.884058
69 AN2 0.48913 0.734177
70 S4M 0.488889 0.831169
71 SRA 0.488636 0.746835
72 LAD 0.485437 0.810127
73 52H 0.484848 0.674157
74 A12 0.483516 0.759494
75 BA3 0.483516 0.74359
76 AP2 0.483516 0.759494
77 AOC 0.483146 0.842857
78 NEC 0.483146 0.788732
79 Y3J 0.481481 0.768116
80 NVA LMS 0.480392 0.696629
81 VRT 0.479167 0.861111
82 50T 0.478723 0.734177
83 5AS 0.478261 0.655556
84 B4P 0.478261 0.74359
85 ADP 0.478261 0.74359
86 AP5 0.478261 0.74359
87 A3N 0.477778 0.830986
88 YSA 0.476636 0.712644
89 XAH 0.476636 0.768293
90 0XU 0.473684 0.897059
91 WAQ 0.471154 0.807692
92 NSS 0.470588 0.712644
93 5AD 0.468354 0.791045
94 ADP MG 0.468085 0.734177
95 AU1 0.468085 0.725
96 M33 0.468085 0.734177
97 MAO 0.467391 0.797468
98 TXA 0.466667 0.759494
99 A3G 0.466667 0.871429
100 NB8 0.466667 0.775
101 3AM 0.465909 0.727273
102 DAL AMP 0.465347 0.779221
103 ATP 0.463158 0.74359
104 ADP BEF 0.463158 0.716049
105 A3T 0.463158 0.842857
106 BEF ADP 0.463158 0.716049
107 ACP 0.463158 0.746835
108 7D7 0.4625 0.785714
109 LEU LMS 0.461538 0.677778
110 APC 0.458333 0.759494
111 AQP 0.458333 0.74359
112 APR 0.458333 0.766234
113 PRX 0.458333 0.746835
114 AR6 0.458333 0.766234
115 5FA 0.458333 0.74359
116 IOT 0.456897 0.761905
117 4AD 0.456311 0.794872
118 PAJ 0.456311 0.722892
119 WSA 0.45614 0.72093
120 FA5 0.453704 0.805195
121 YAP 0.453704 0.794872
122 RBY 0.453608 0.782051
123 ADV 0.453608 0.782051
124 ADP PO3 0.453608 0.763158
125 AD9 0.453608 0.725
126 SAP 0.453608 0.728395
127 AGS 0.453608 0.728395
128 PTJ 0.45283 0.731707
129 MHZ 0.452632 0.797468
130 00A 0.451923 0.740741
131 A3P 0.451613 0.74026
132 YLP 0.451327 0.771084
133 7MD 0.45045 0.768293
134 ALF ADP 0.45 0.707317
135 ADP ALF 0.45 0.707317
136 ATP MG 0.44898 0.734177
137 2VA 0.447917 0.819444
138 OOB 0.446602 0.779221
139 ANP 0.444444 0.725
140 ACQ 0.444444 0.746835
141 TAT 0.444444 0.7375
142 P5A 0.443396 0.719101
143 7D5 0.443182 0.708861
144 ARG AMP 0.442478 0.759036
145 A1R 0.442308 0.7625
146 YLC 0.439655 0.790123
147 2AM 0.438202 0.717949
148 DLL 0.438095 0.779221
149 A22 0.436893 0.734177
150 D3Y 0.436893 0.859155
151 TYR AMP 0.436364 0.782051
152 ATF 0.435644 0.716049
153 MYR AMP 0.435185 0.746988
154 SO8 0.434343 0.808219
155 3UK 0.433962 0.769231
156 OAD 0.433962 0.769231
157 TAD 0.433628 0.765432
158 25A 0.432692 0.74359
159 ANP MG 0.431373 0.707317
160 VO4 ADP 0.431373 0.734177
161 ADP VO4 0.431373 0.734177
162 9SN 0.431193 0.731707
163 TYM 0.431034 0.805195
164 PR8 0.429907 0.8
165 ADQ 0.428571 0.746835
166 YLB 0.42735 0.771084
167 3OD 0.425926 0.769231
168 FYA 0.425926 0.779221
169 1ZZ 0.425926 0.746988
170 PPS 0.425743 0.674419
171 NVA 2AD 0.424242 0.808219
172 MAP 0.423077 0.707317
173 A2P 0.421053 0.727273
174 4YB 0.421053 0.735632
175 ADP BMA 0.420561 0.746835
176 5SV 0.419048 0.731707
177 3NZ 0.416667 0.824324
178 YLA 0.416667 0.771084
179 48N 0.413793 0.753086
180 LPA AMP 0.413793 0.768293
181 AYB 0.413223 0.761905
182 QQY 0.413043 0.696203
183 ACK 0.413043 0.710526
184 JB6 0.412844 0.7625
185 BIS 0.412844 0.719512
186 PAP 0.41 0.730769
187 OVE 0.408602 0.7125
188 4UV 0.40708 0.75
189 AMP DBH 0.40708 0.746835
190 3AD 0.406977 0.852941
191 AF3 ADP 3PG 0.40678 0.743902
192 OMR 0.40678 0.738095
193 LAQ 0.405172 0.768293
194 A A 0.40367 0.74359
195 7C5 0.403509 0.789474
196 7MC 0.403361 0.75
197 4UU 0.4 0.75
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3I53; Ligand: SAH; Similar sites found: 192
This union binding pocket(no: 1) in the query (biounit: 3i53.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1LSS NAD 0.003472 0.41009 1.20482
2 2DPM SAM 0.001185 0.43147 1.40845
3 4AZT SAM 0.0001706 0.47394 1.80723
4 2EJU SAH 0.0002934 0.46371 1.80723
5 1ORR NAD 0.005276 0.41845 1.80723
6 5FTW SAH 0.0002714 0.45626 1.95312
7 2HMT NAI 0.005953 0.40204 2.08333
8 4AZW SAM 0.000116 0.46627 2.10843
9 1G55 SAH 0.0002096 0.46539 2.10843
10 5XLX SAH 0.0003994 0.44077 2.10843
11 3LCV SAM 0.00003096 0.50003 2.13523
12 5D9X GSH 0.01892 0.41242 2.17391
13 5KOK SAH 0.00000325 0.54237 2.40964
14 4KIB SAH 0.000005632 0.5058 2.40964
15 5E72 SAM 0.00003813 0.49405 2.40964
16 1KPH SAH 0.0006303 0.44297 2.40964
17 3A27 SAM 0.00117 0.43761 2.40964
18 1KPG SAH 0.0006375 0.43525 2.40964
19 5KOK R9T 0.00006532 0.41574 2.40964
20 5KOK S9T 0.00006389 0.41186 2.40964
21 4B1Y LAB 0.01468 0.41143 2.40964
22 4EUE NAI 0.008165 0.40891 2.40964
23 3S1S SAH 0.003133 0.4011 2.40964
24 3GDN HBX 0.02854 0.40085 2.40964
25 3GDN FAD 0.02086 0.40085 2.40964
26 3A25 SAM 0.001129 0.43828 2.65781
27 4KRG SAH 0.0000325 0.47694 2.71084
28 5DX0 SFG 0.0001931 0.4703 2.71084
29 5DWQ SFG 0.0001768 0.47007 2.71084
30 2P41 SAH 0.0002533 0.46648 2.71084
31 5JJR SAH 0.0003169 0.46225 2.71084
32 5DX8 SFG 0.0001299 0.45691 2.71084
33 4XUC 43G 0.0008499 0.45464 2.71084
34 4XUC SAM 0.0008499 0.45464 2.71084
35 5ULP KB1 0.00009885 0.45345 2.71084
36 5DXA SFG 0.0001689 0.45219 2.71084
37 5DX1 SFG 0.0001273 0.44464 2.71084
38 2WPF FAD 0.03737 0.4145 2.71084
39 4XFR CIT 0.02266 0.40403 2.71084
40 2WA2 SAM 0.0006912 0.42459 2.89855
41 3EVG SAH 0.0001634 0.4547 2.90909
42 2OG2 MLI 0.004308 0.44336 3.01205
43 1SQF SAM 0.001878 0.42866 3.01205
44 3VSE SAH 0.0008807 0.40387 3.01205
45 2PXX SAH 0.0001032 0.47848 3.25581
46 1GXU 2HP 0.008609 0.4048 3.2967
47 3B9Q MLI 0.007793 0.43473 3.31126
48 5E8J SAH 0.0001758 0.48903 3.31325
49 4OBW SAM 0.0002008 0.47086 3.31325
50 5T67 JHZ 0.001712 0.45315 3.31325
51 5T67 SAH 0.001325 0.45315 3.31325
52 5E9W SAH 0.0001244 0.43795 3.31325
53 2PWY SAH 0.001062 0.4353 3.31325
54 2PZM UDP 0.01697 0.40582 3.33333
55 2PZM NAD 0.01697 0.40582 3.33333
56 2PX8 SAH 0.001513 0.41612 3.34572
57 5BW4 SAM 0.00002931 0.47733 3.37079
58 2Y91 98J 0.02889 0.40376 3.39623
59 1SB8 UD2 0.02754 0.40228 3.40909
60 1SB8 NAD 0.02382 0.40228 3.40909
61 1NW5 SAM 0.004419 0.4037 3.44828
62 1Q0S SAH 0.002386 0.42214 3.4749
63 1TPY SAH 0.0005651 0.44496 3.48432
64 1XTP SAI 0.00008809 0.46654 3.54331
65 1VE3 SAM 0.0000007271 0.5769 3.61446
66 3BXO SAM 0.000007155 0.48627 3.61446
67 5THZ SAH 0.0001258 0.47436 3.61446
68 5THY SAH 0.0001895 0.46276 3.61446
69 1DL5 SAH 0.0005517 0.45256 3.61446
70 3LKZ SFG 0.0006507 0.44446 3.61446
71 1Z3C SA8 0.00004054 0.50649 3.69128
72 2ZFU SAH 0.00002255 0.5013 3.72093
73 2A14 SAH 0.001327 0.4294 3.80228
74 3GCZ SAM 0.0001146 0.46052 3.91566
75 1ELI PYC 0.01581 0.40264 3.91566
76 3FZG SAM 0.00007538 0.50023 4
77 3GEG NAD 0.003963 0.41732 4.04858
78 5F8F SFG 0.00001604 0.53072 4.21687
79 3MQ2 SAH 0.00001741 0.5229 4.21687
80 5HJM MTA 0.00006818 0.48614 4.21687
81 4DMG SAM 0.0007218 0.46569 4.21687
82 4UCI SAM 0.002721 0.41801 4.21687
83 1G60 SAM 0.002199 0.42195 4.23077
84 5GVR LMR 0.00721 0.43101 4.2735
85 2ZIF SAM 0.0009733 0.42844 4.3771
86 4KRI SAH 0.000004949 0.52875 4.38799
87 5MGZ SAH 0.000001792 0.55336 4.51807
88 5X62 SAH 0.000006893 0.54075 4.51807
89 3G2O SAM 0.000009211 0.529 4.51807
90 5XVQ SAH 0.001152 0.4195 4.51807
91 2PT9 2MH 0.007384 0.41318 4.51807
92 2PT9 S4M 0.004982 0.41011 4.51807
93 1L1E SAH 0.00074 0.4381 4.52962
94 4NEC SAH 0.000005902 0.55042 4.54545
95 3DXY SAM 0.000005033 0.56818 4.58716
96 1L3I SAH 0.001054 0.44051 4.6875
97 1T27 PCW 0.00568 0.42563 4.79705
98 3QOX SAH 0.00003508 0.49774 4.81928
99 5XVK SAH 0.0004414 0.43553 4.81928
100 4HXY NDP 0.008563 0.40679 4.81928
101 5MW4 5JU 0.0001033 0.40453 4.81928
102 1R18 SAH 0.00047 0.43964 4.84582
103 5K7U SAM 0.004819 0.41087 4.88889
104 4II2 ATP 0.001289 0.42805 4.90798
105 4PIO SAH 0.000005014 0.55295 4.95356
106 4PIO AVI 0.000004971 0.55143 4.95356
107 3MB5 SAM 0.001034 0.42157 5.09804
108 3PT9 SAH 0.001517 0.41591 5.12048
109 1R37 NAD 0.009578 0.40818 5.12048
110 5IL1 SAM 0.006805 0.40433 5.33333
111 1XKQ NDP 0.01341 0.40058 5.35714
112 4PSR FUL 0.01924 0.41406 5.42169
113 4RDI ATP 0.004479 0.41225 5.42169
114 4D79 ATP 0.004783 0.411 5.42169
115 4RDH AMP 0.008139 0.40789 5.42169
116 3HVJ 705 0.001059 0.45412 5.42986
117 4LWP SAH 0.0001038 0.46372 5.43478
118 2DTX BMA 0.01132 0.41016 5.68182
119 2UYQ SAM 0.000008951 0.58578 5.72289
120 3BGD SAH 0.00004588 0.47417 5.76923
121 3BGD PM6 0.00008553 0.43986 5.76923
122 3H2B SAH 0.00002758 0.49183 5.91133
123 3JWH SAH 0.0000006283 0.51086 6.0241
124 5UAO FAD 0.01892 0.40099 6.0241
125 1R6D DAU 0.009323 0.42429 6.3253
126 1R6D NAD 0.009674 0.42429 6.3253
127 1FEC FAD 0.01055 0.41784 6.3253
128 5KVA SAM 0.003716 0.40379 6.47482
129 1F3L SAH 0.00009166 0.46893 6.54206
130 5DNK SAH 0.000002451 0.48746 6.62651
131 3U4C NDP 0.001925 0.4323 6.62651
132 4DCM SAM 0.0004948 0.42455 6.62651
133 5GM1 SAH 0.00000274 0.52088 6.73401
134 1JG3 ADN 0.0008028 0.44471 6.80851
135 4CS9 AMP 0.004269 0.45091 6.87831
136 2VDV SAM 0.0000003081 0.61698 6.92771
137 3OU2 SAH 0.00003808 0.46376 7.33945
138 5CUQ NSC 0.0006277 0.45774 7.49064
139 2YX1 SFG 0.0002539 0.48162 7.53012
140 2BZG SAH 0.0001138 0.46213 7.75862
141 3T7S SAM 0.0000008632 0.54365 7.83133
142 5FA8 SAM 0.00002931 0.48113 8.07453
143 5L2J 70E 0.0259 0.4106 8.16327
144 5L2J 6UL 0.02446 0.4106 8.16327
145 2HNK SAH 0.001871 0.4213 8.3682
146 5MPT SAH 0.0006691 0.44815 8.43373
147 1BC5 SAH 0.001593 0.42787 8.55019
148 5E1M SAH 0.0003785 0.45024 8.71369
149 1I1N SAH 0.0000846 0.48922 8.73494
150 4N49 SAM 0.0008972 0.43461 8.73494
151 4UXM BE7 0.002887 0.41386 8.73494
152 4YMH SAH 0.002268 0.41781 9.03614
153 5LOG SAH 0.004366 0.40926 9.44206
154 3P2E SAH 0.00006 0.48358 9.63855
155 2AQJ FAD 0.02359 0.40949 9.63855
156 2AQJ TRP 0.02286 0.40949 9.63855
157 1Y8Q ATP 0.002651 0.40195 9.63855
158 4TQG NDP 0.001789 0.43367 9.90712
159 2AOT SAH 0.00002729 0.47429 10.8434
160 1JQD HSM 0.0001813 0.43119 10.8434
161 3L9W AMP 0.003437 0.42411 10.8434
162 1JQD SAH 0.0002512 0.41144 10.8434
163 3C6K MTA 0.01036 0.40884 10.8434
164 3C6K SPD 0.01036 0.40884 10.8434
165 5L95 AMP 0.003259 0.41467 11.25
166 1WMA AB3 0.02188 0.40075 11.5942
167 1QAN SAH 0.001016 0.42684 11.8852
168 4BLW AMP 0.001323 0.44617 12.8028
169 4BLW SAH 0.001188 0.43828 12.8028
170 1U2Z SAH 0.0003463 0.45582 13.253
171 5GWX SAM 0.00141 0.40327 13.5542
172 5GWX SAR 0.00141 0.40327 13.5542
173 2XVM SAH 0.00003557 0.46477 13.5678
174 1UAY ADN 0.0005699 0.46532 14.0496
175 5JGL SAM 0.0002831 0.46914 14.1566
176 2IV2 MGD 0.009698 0.41012 14.759
177 4PNE SAH 0.000004151 0.51412 15.6627
178 1O97 AMP 0.01494 0.41687 16.25
179 4R6W SAH 0.0000109 0.44585 17.1687
180 4A6D SAM 0.0000000001207 0.73082 21.3855
181 4GQB 0XU 0.00006154 0.48949 31.8182
182 5FA5 MTA 0.0002991 0.47307 35
183 4E70 N7I 0.0000000455 0.53365 37.9518
184 3TKY SAH 0.000000000005062 0.76521 40.9639
185 1KYZ SAH 0.00000001295 0.61859 40.9639
186 1KYZ FER 0.000000426 0.58806 40.9639
187 3LST SAH 0.00000000001566 0.81631 42.2414
188 1FP1 SAH 0.00000000002781 0.69391 43.3735
189 1ZGA SAH 0.0000000481 0.56716 44.8795
190 3P9C SAH 0.000000009046 0.5357 46.6867
191 3GXO SAH 0.00000000009326 0.76827 46.988
192 3GWZ SAH 0.00000000001517 0.68829 46.988
Pocket No.: 2; Query (leader) PDB : 3I53; Ligand: SAH; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3i53.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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