Receptor
PDB id Resolution Class Description Source Keywords
1NEY 1.2 Å EC: 5.3.1.1 TRIOSEPHOSPHATE ISOMERASE IN COMPLEX WITH DHAP SACCHAROMYCES CEREVISIAE YEAST TRIOSEPHOSPHATE ISOMERASE DHAP DIHYDROXYACETONE PHOSPHATE MICHAELIS COMPLEX
Ref.: OPTIMAL ALIGNMENT FOR ENZYMATIC PROTON TRANSFER: STRUCTURE OF THE MICHAELIS COMPLEX OF TRIOSEPHOSPHATE ISOMERASE AT 1.2-A RESOLUTION. PROC.NATL.ACAD.SCI.USA V. 100 50 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
13P A:5001;
B:6001;
Valid;
Valid;
none;
none;
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170.058 C3 H7 O6 P C(C(=...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2YPI 2.5 Å EC: 5.3.1.1 CRYSTALLOGRAPHIC ANALYSIS OF THE COMPLEX BETWEEN TRIOSEPHOSPHATE ISOMERASE AND 2-PHOSPHOGLYCOLATE AT 2.5- A NGSTROMS RESOLUTION. IMPLICATIONS FOR CATALYSIS SACCHAROMYCES CEREVISIAE TRIOSE PHOSPHATE ISOMERASE
Ref.: CRYSTALLOGRAPHIC ANALYSIS OF THE COMPLEX BETWEEN TRIOSEPHOSPHATE ISOMERASE AND 2-PHOSPHOGLYCOLATE AT 2.5-A RESOLUTION: IMPLICATIONS FOR CATALYSIS. BIOCHEMISTRY V. 29 6619 1990
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 1NF0 - 13P C3 H7 O6 P C(C(=O)COP....
2 7TIM - PGH C2 H6 N O6 P C(C(=O)NO)....
3 2YPI Ki = 15 uM PGA C2 H5 O6 P C(C(=O)O)O....
4 1NEY - 13P C3 H7 O6 P C(C(=O)COP....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 1NF0 - 13P C3 H7 O6 P C(C(=O)COP....
2 7TIM - PGH C2 H6 N O6 P C(C(=O)NO)....
3 2YPI Ki = 15 uM PGA C2 H5 O6 P C(C(=O)O)O....
4 1NEY - 13P C3 H7 O6 P C(C(=O)COP....
50% Homology Family (62)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1IIH Ki = 1.3 mM 3PG C3 H7 O7 P C([C@H](C(....
2 2X1T - RES C4 H10 N O8 P C([C@H]([C....
3 5I3K Ki = 12 uM PGA C2 H5 O6 P C(C(=O)O)O....
4 2VEL - PGA C2 H5 O6 P C(C(=O)O)O....
5 5I3I Ki = 2.6 mM PGA C2 H5 O6 P C(C(=O)O)O....
6 2V2C Ki = 0.39 mM PGA C2 H5 O6 P C(C(=O)O)O....
7 2VEN - CIT C6 H8 O7 C(C(=O)O)C....
8 5I3H Ki = 120 uM PGA C2 H5 O6 P C(C(=O)O)O....
9 2X1S - X1S C3 H6 O5 S C(CS(=O)(=....
10 1KV5 Ki = 60 uM PGA C2 H5 O6 P C(C(=O)O)O....
11 4TIM Ki = 6.9 mM 2PG C3 H7 O7 P C([C@H](C(....
12 1TTJ - PGH C2 H6 N O6 P C(C(=O)NO)....
13 6TIM Ki = 0.61 mM G3P C3 H9 O6 P C([C@H](CO....
14 1TRD Ki = 4 uM PGH C2 H6 N O6 P C(C(=O)NO)....
15 2VEK - CIT C6 H8 O7 C(C(=O)O)C....
16 2V2H Ki = 0.17 mM PGA C2 H5 O6 P C(C(=O)O)O....
17 2J27 Ki = 0.3 mM PGA C2 H5 O6 P C(C(=O)O)O....
18 4PC8 - GOA C2 H4 O3 C(C(=O)O)O
19 2X1R - X1R C6 H12 O4 S CCCS(=O)(=....
20 2X2G - 3PG C3 H7 O7 P C([C@H](C(....
21 1TTI - PGA C2 H5 O6 P C(C(=O)O)O....
22 1NF0 - 13P C3 H7 O6 P C(C(=O)COP....
23 7TIM - PGH C2 H6 N O6 P C(C(=O)NO)....
24 2YPI Ki = 15 uM PGA C2 H5 O6 P C(C(=O)O)O....
25 1NEY - 13P C3 H7 O6 P C(C(=O)COP....
26 2BTM - PGA C2 H5 O6 P C(C(=O)O)O....
27 5EYW - PGA C2 H5 O6 P C(C(=O)O)O....
28 4YMZ - 13P C3 H7 O6 P C(C(=O)COP....
29 3UWV - 2PG C3 H7 O7 P C([C@H](C(....
30 3UWW - 3PG C3 H7 O7 P C([C@H](C(....
31 3UWZ - G2H C3 H9 O6 P C(C(CO)OP(....
32 3M9Y - CIT C6 H8 O7 C(C(=O)O)C....
33 3UWU - G3P C3 H9 O6 P C([C@H](CO....
34 1LYX Ki = 0.029 mM PGA C2 H5 O6 P C(C(=O)O)O....
35 1O5X - 3PY C3 H4 O4 C(C(=O)C(=....
36 2VFH - 3PG C3 H7 O7 P C([C@H](C(....
37 1M7O - 3PG C3 H7 O7 P C([C@H](C(....
38 2VFE - 3PG C3 H7 O7 P C([C@H](C(....
39 2VFI Ki = 1.9 mM 3PG C3 H7 O7 P C([C@H](C(....
40 1M7P - G3H C3 H7 O6 P C([C@H](C=....
41 3PVF - PGA C2 H5 O6 P C(C(=O)O)O....
42 2VFG - 3PG C3 H7 O7 P C([C@H](C(....
43 3TAO Kd = 7.28 uM PGH C2 H6 N O6 P C(C(=O)NO)....
44 1SUX - BTS C10 H11 N O3 S3 c1ccc2c(c1....
45 1TPW Ki = 0.5 mM PGH C2 H6 N O6 P C(C(=O)NO)....
46 1SW3 - PGA C2 H5 O6 P C(C(=O)O)O....
47 1TPB - PGH C2 H6 N O6 P C(C(=O)NO)....
48 1SW0 - PGA C2 H5 O6 P C(C(=O)O)O....
49 1TPH - PGH C2 H6 N O6 P C(C(=O)NO)....
50 1TPU - PGH C2 H6 N O6 P C(C(=O)NO)....
51 1TPV - PGH C2 H6 N O6 P C(C(=O)NO)....
52 1SW7 - PGA C2 H5 O6 P C(C(=O)O)O....
53 1TPC - PGH C2 H6 N O6 P C(C(=O)NO)....
54 2VXN - PGA C2 H5 O6 P C(C(=O)O)O....
55 2Y62 - G3P C3 H9 O6 P C([C@H](CO....
56 1AMK Ki = 0.05 mM PGA C2 H5 O6 P C(C(=O)O)O....
57 2Y61 - G3P C3 H9 O6 P C([C@H](CO....
58 1QDS Ki = 0.048 mM PGA C2 H5 O6 P C(C(=O)O)O....
59 1N55 - PGA C2 H5 O6 P C(C(=O)O)O....
60 1IF2 - 129 C3 H8 N O5 P C(CP(=O)(O....
61 4BI6 Kd = 113.3 uM PGA C2 H5 O6 P C(C(=O)O)O....
62 4BI7 Kd = 26.4 uM PGA C2 H5 O6 P C(C(=O)O)O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 13P; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 13P 1 1
2 PGA 0.5 0.818182
3 HPV 0.4375 0.90625
4 PGH 0.424242 0.622222
5 IBS 0.404255 0.815789
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2YPI; Ligand: PGA; Similar sites found: 238
This union binding pocket(no: 1) in the query (biounit: 2ypi.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1GVF PGH 0.0002101 0.46599 None
2 4QYS PLP SEP 0.004844 0.43585 1.21457
3 4QYS PLR 0.003438 0.42543 1.21457
4 4MSG 2C6 0.007614 0.43797 1.38249
5 1V0O INR 0.009517 0.41099 1.61943
6 4USR FAD 0.02607 0.40938 1.61943
7 1NJJ ORX 0.001499 0.45566 2.02429
8 1TB3 FMN 0.006052 0.43818 2.02429
9 1GY8 NAD 0.007367 0.43513 2.02429
10 2XVF FAD 0.02607 0.41347 2.02429
11 1F76 FMN 0.01518 0.41267 2.02429
12 3CQD ATP 0.0395 0.40401 2.02429
13 2FLI DX5 0.001015 0.46391 2.27273
14 4J3L AJ5 0.005459 0.42259 2.38095
15 2Z6I FMN 0.000003873 0.5842 2.42915
16 2Z6J FMN 0.00001732 0.56466 2.42915
17 2B4G FMN 0.006676 0.43193 2.42915
18 3LZW NAP 0.02445 0.42991 2.42915
19 3C3N FMN 0.01223 0.4285 2.42915
20 1OYB FMN 0.01003 0.41864 2.42915
21 1OYB HBA 0.0123 0.41864 2.42915
22 1DJN FMN 0.01054 0.41757 2.42915
23 1Q1R FAD 0.04174 0.40274 2.42915
24 4OSP NAP 0.0291 0.40234 2.42915
25 2HQU DUP 0.01514 0.40491 2.43902
26 4K90 MLA 0.01621 0.40412 2.7907
27 4EWN 0VR 0.0000729 0.50978 2.83401
28 3KRU FMN 0.001018 0.48007 2.83401
29 3W9Z FMN 0.0006007 0.47081 2.83401
30 3MJY IJZ 0.001653 0.46937 2.83401
31 3MJY FMN 0.001653 0.46937 2.83401
32 1AL8 DHP 0.003066 0.4531 2.83401
33 1AL8 FMN 0.002031 0.45283 2.83401
34 4QNW FMN 0.001779 0.45204 2.83401
35 1T3Q FAD 0.007949 0.44028 2.83401
36 1P4C FMN 0.007333 0.43523 2.83401
37 1Z45 NAD 0.01239 0.42241 2.83401
38 4I9A NCN 0.005754 0.4215 2.83401
39 4BNU 9KQ 0.01497 0.40847 2.83401
40 4J7H TLO 0.01531 0.40637 2.83401
41 5TCI MLI 0.0007916 0.40608 2.83401
42 1OFD FMN 0.0003307 0.50903 3.23887
43 1OFD AKG 0.0007981 0.4868 3.23887
44 1PVN MZP 0.002346 0.46989 3.23887
45 1JCM 137 0.0008422 0.46152 3.23887
46 1X1Z BMP 0.006447 0.45441 3.23887
47 1NHX FTB 0.01259 0.43471 3.23887
48 1NHX PEP 0.0121 0.43471 3.23887
49 3ATY FMN 0.006784 0.4286 3.23887
50 2Q8Z NUP 0.007287 0.42549 3.23887
51 1Q0H NDP 0.03474 0.41536 3.23887
52 1Q0H FOM 0.03253 0.41536 3.23887
53 4YSW FAD 0.04407 0.41525 3.23887
54 3NTD FAD 0.03045 0.41088 3.23887
55 1QO8 FAD 0.03601 0.41056 3.23887
56 3H4L ANP 0.01365 0.40881 3.23887
57 5KF6 FAD 0.02984 0.40634 3.23887
58 5KF6 TFB 0.02984 0.40634 3.23887
59 2NLI FMN 0.01841 0.40558 3.23887
60 2NLI LAC 0.02395 0.4054 3.23887
61 1YNQ NDP 0.02358 0.40444 3.23887
62 3T6E MQ9 0.03131 0.40306 3.23887
63 3EXS 5RP 0.0000524 0.50761 3.61991
64 4Q4K FMN 0.000002433 0.60115 3.64372
65 3KDN CAP 0.0008623 0.49977 3.64372
66 5GJO PLP 0.0002974 0.47812 3.64372
67 1LBF 137 0.001067 0.47167 3.64372
68 2OO0 PLP 0.001312 0.45003 3.64372
69 1TUF AZ1 0.004941 0.43542 3.64372
70 1EP2 ORO 0.01018 0.43149 3.64372
71 1EP2 FMN 0.007992 0.42941 3.64372
72 5OCS FMN 0.00441 0.42906 3.64372
73 4N02 FNR 0.01282 0.41488 3.64372
74 2GOU FMN 0.02205 0.41313 3.64372
75 4JIQ 1L5 0.01674 0.41055 3.64372
76 4JIQ FMN 0.01674 0.41055 3.64372
77 4O8A FAD 0.02297 0.40996 3.64372
78 1TIW TFB 0.033 0.40904 3.64372
79 1TIW FAD 0.033 0.40904 3.64372
80 2XGT NSS 0.02207 0.40588 3.64372
81 4M5P FMN 0.01898 0.40178 3.64372
82 1LQA NDP 0.03883 0.40145 3.64372
83 1M5W DXP 0.001337 0.42732 3.7037
84 1DBT U5P 0.001532 0.45121 3.76569
85 3CTL S6P 0.001856 0.44921 3.8961
86 4P5E N6P 0.01136 0.41272 3.94737
87 1OVD FMN 0.0009295 0.48724 4.04858
88 1OVD ORO 0.0009295 0.48724 4.04858
89 4CW5 FMN 0.001629 0.44992 4.04858
90 1VYP FMN 0.003218 0.44623 4.04858
91 1VYP TNF 0.002989 0.44623 4.04858
92 5U61 7WG 0.009138 0.43502 4.04858
93 1B57 PGH 0.002327 0.4308 4.04858
94 3ITJ FAD 0.02753 0.42229 4.04858
95 4XP7 FNR 0.006358 0.42138 4.04858
96 3HDY FDA 0.04736 0.41596 4.04858
97 3HDY GDU 0.04851 0.41596 4.04858
98 4D57 ARG AMP 0.02415 0.4132 4.04858
99 3QH2 3NM 0.003165 0.41311 4.0724
100 1BKJ FMN 0.01806 0.40889 4.16667
101 2F6U CIT 0.00005165 0.52284 4.2735
102 3OVR 5SP 0.0003117 0.49093 4.38596
103 1UZD CAP 0.003196 0.43964 4.45344
104 2V63 CAP 0.003674 0.43668 4.45344
105 2V6A CAP 0.003698 0.43469 4.45344
106 2V67 CAP 0.004518 0.4323 4.45344
107 2FJK 13P 0.002996 0.42568 4.45344
108 3AXB PRO 0.03646 0.41027 4.45344
109 3AXB FAD 0.03 0.41027 4.45344
110 2E5V FAD 0.04628 0.40712 4.45344
111 4ADC PLP 0.01748 0.4067 4.45344
112 5H2U 1N1 0.0163 0.40158 4.45344
113 3KJD 78P 0.02089 0.40133 4.45344
114 2OEM 1AE 0.0009384 0.45193 4.8583
115 2Q3R FMN 0.003639 0.43503 4.8583
116 1WDD CAP 0.004052 0.43276 4.8583
117 4ORM 2V6 0.02695 0.43009 4.8583
118 4ORM FMN 0.02695 0.43009 4.8583
119 4ORM ORO 0.02695 0.43009 4.8583
120 1I2B NAD 0.02705 0.42553 4.8583
121 1N62 FAD 0.0183 0.42247 4.8583
122 2AQJ TRP 0.04017 0.41809 4.8583
123 2AQJ FAD 0.04122 0.41809 4.8583
124 3NC9 TR3 0.02791 0.41287 4.8583
125 1SFF IK2 0.01416 0.40633 4.8583
126 5VSM MET 0.01445 0.4059 4.8583
127 5VSM 5AD 0.0165 0.40309 4.8583
128 4NAE 1GP 0.00001045 0.49223 4.88889
129 3HYK A3P 0.009245 0.4052 4.91803
130 1BWV CAP 0.004358 0.4293 5.07246
131 4UTU LRY 0.000007215 0.55449 5.24017
132 4UTW RFW 0.000009439 0.55204 5.24017
133 2QCD U5P 0.001744 0.45053 5.26316
134 3MI2 PFU 0.007938 0.44961 5.26316
135 4HKP TKW 0.0022 0.44937 5.26316
136 4HKP 16B 0.002005 0.44558 5.26316
137 2VDH CAP 0.003897 0.43543 5.26316
138 1PS9 FMN 0.004982 0.43197 5.26316
139 2GJN FMN 0.00002586 0.42685 5.26316
140 1Q9I TEO 0.03362 0.4217 5.26316
141 2GJN NIS 0.00002535 0.41568 5.26316
142 5HSA FAS 0.03649 0.40941 5.26316
143 4JNA FAD 0.03837 0.40909 5.26316
144 1O94 ADP 0.02115 0.40405 5.26316
145 3QMN COA 0.003013 0.43901 5.42636
146 1Q6O LG6 0.000151 0.49473 5.55556
147 3VKC FPQ 0.0004098 0.4831 5.66802
148 1ICP FMN 0.0009516 0.47726 5.66802
149 2HSA FMN 0.001348 0.46965 5.66802
150 2NVA PL2 0.001124 0.46892 5.66802
151 1ME8 RVP 0.002264 0.46734 5.66802
152 3OIX FMN 0.003848 0.43917 5.66802
153 3QVP FAD 0.03086 0.41497 5.66802
154 4NMC 2OP 0.0317 0.40805 5.66802
155 4NMC FAD 0.03308 0.40805 5.66802
156 5G5G FAD 0.04047 0.40702 5.66802
157 2H8H H8H 0.01539 0.40093 5.66802
158 1F5V FMN 0.0117 0.40858 5.83333
159 1FIQ FAD 0.0374 0.4023 5.93607
160 4WZH FMN 0.001429 0.46374 6.07287
161 2RDT FMN 0.00216 0.45483 6.07287
162 2RDT 2RD 0.003011 0.45483 6.07287
163 3N9R TD3 0.002384 0.43031 6.07287
164 3C56 PH4 0.005766 0.42532 6.07287
165 3WQD PLP 999 0.00207 0.40662 6.07287
166 4X9X OLA 0.02069 0.40594 6.07287
167 1Z41 FMN 0.001784 0.44366 6.47773
168 1Z48 FMN 0.002025 0.44105 6.47773
169 1Z44 FMN 0.002244 0.41365 6.47773
170 4PJT 2YQ 0.03228 0.40239 6.47773
171 5F7R GLC GLC 0.01763 0.40168 6.47773
172 1IR1 CAP 0.002801 0.44054 6.50407
173 1EIX BMQ 0.003044 0.43477 6.53061
174 2GKS ADP 0.01341 0.4092 6.88259
175 5EB4 FAD 0.03769 0.40866 6.88259
176 4YSX FAD 0.03764 0.40783 6.88259
177 2BLE 5GP 0.0004098 0.49404 7.28745
178 1DQX BMP 0.002576 0.4442 7.28745
179 5XDT ZI7 0.007439 0.42958 7.28745
180 2WET FAD 0.03637 0.41033 7.28745
181 4N65 FMN 0.02795 0.40323 7.28745
182 2Y88 2ER 0.0002761 0.51305 7.37705
183 1QPR PPC 0.01307 0.40975 7.69231
184 1GTE IUR 0.00183 0.46969 8.09717
185 1GTE FMN 0.00183 0.46969 8.09717
186 3HF3 FMN 0.003757 0.43798 8.09717
187 4IXH IMP 0.0007975 0.47281 8.50202
188 1GXS BEZ 0.003275 0.40444 8.50202
189 1KBI PYR 0.003641 0.44508 8.90688
190 1KBJ FMN 0.003427 0.44487 8.90688
191 3BXF 13P 0.003775 0.43028 8.90688
192 2VAP GDP 0.01757 0.41347 8.90688
193 1KBI FMN 0.04884 0.41278 8.90688
194 1G51 AMO 0.02559 0.40264 8.90688
195 1UZH CAP 0.004349 0.43311 9.01639
196 2O4N TPV 0.009681 0.42243 9.09091
197 4AF0 IMP 0.0002338 0.49704 9.31174
198 5X8G S0N 0.03811 0.41393 9.31174
199 4BUY F37 0.004495 0.44335 9.58333
200 2TPS TPS 0.02563 0.40127 9.69163
201 1D4D FAD 0.01055 0.43964 9.7166
202 4TMC FMN 0.01952 0.40279 9.7166
203 1UJP CIT 0.001215 0.4125 9.9631
204 2PLK P3D 0.002427 0.44546 10.1215
205 3HRD FAD 0.02499 0.41812 10.1215
206 3Q9T FAY 0.02721 0.41345 10.1215
207 2WW4 ADP 0.009734 0.40414 10.1215
208 3HRD MCN 0.03528 0.40362 10.1215
209 2FXU ATP 0.03145 0.42456 10.5263
210 4PHR UDP 0.01588 0.40876 10.5263
211 1GPE FAD 0.04449 0.40805 10.5263
212 4YC0 5OF 0.01791 0.40464 10.5263
213 3BW2 FMN 0.000001984 0.61391 10.9312
214 2CH5 NAG 0.01149 0.40075 10.9312
215 3KO8 NAD 0.02706 0.40745 11.336
216 2Q3O FMN 0.0004024 0.4855 11.7409
217 4IGH 1EA 0.02222 0.43529 11.7409
218 4IGH FMN 0.02222 0.43529 11.7409
219 4IGH ORO 0.02222 0.43529 11.7409
220 1Q0S SAH 0.01505 0.41142 11.7409
221 4UI8 IY5 0.004232 0.42992 12.0419
222 5ODQ 9SB 0.01563 0.4106 12.1429
223 3B0P FMN 0.0001681 0.49251 12.1457
224 1UUO FMN 0.01711 0.4356 13.7652
225 1UUO ORO 0.01711 0.4356 13.7652
226 1UUO BRF 0.01816 0.4356 13.7652
227 4YRY FAD 0.01697 0.42787 13.7652
228 4YRY NAD 0.02378 0.42787 13.7652
229 5HQ0 LZ9 0.008345 0.41752 14.2857
230 5A5W GUO 0.00006118 0.55208 14.5749
231 1SB8 NAD 0.0485 0.40753 14.9798
232 2C6Q IMP 0.0004865 0.48521 15.7895
233 2C6Q NDP 0.001387 0.48494 15.7895
234 4JEJ 1GP 0.000008449 0.548 18.0328
235 1RBL CAP 0.003666 0.4385 19.2661
236 2F5Z FAD 0.04831 0.40455 20.3125
237 2V2V V12 0.03786 0.4077 21.0526
238 2FXD DR7 0.0298 0.40182 23.2323
Pocket No.: 2; Query (leader) PDB : 2YPI; Ligand: PGA; 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: 2ypi.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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