Receptor
PDB id Resolution Class Description Source Keywords
2IV2 2.27 Å EC: 1.2.1.2 REINTERPRETATION OF REDUCED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI ESCHERICHIA COLI OXIDOREDUCTASE 4FE-4S NAEROBIC COMPLETE PROTEOME DEHYDROGENASE DIRECT PROTEIN SEQUENCING FE4S4 FORMATE IRON IRON SULFUR CLUSTER IRON-SULFUR METAL-BINDING MGD MOLYBDENUM MOLYBDOPTERIN MOLYBDOPTERIN GUANINE DINUCLEOTIDE MPT NAD SECYS SELENIUM SELENOCYSTEINE
Ref.: FORMATE-REDUCED E. COLI FORMATE DEHYDROGENASE H: THE REINTERPRETATION OF THE CRYSTAL STRUCTURE SUGGESTS A NEW REACTION MECHANISM. J.BIOL.INORG.CHEM. V. 11 849 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
2MD X:801;
Valid;
none;
submit data
742.573 C20 H28 N10 O13 P2 S2 c1nc2...
MGD X:802;
Valid;
none;
submit data
740.557 C20 H26 N10 O13 P2 S2 c1nc2...
MO X:803;
Invalid;
none;
submit data
95.94 Mo [Mo]
SF4 X:800;
Part of Protein;
none;
submit data
351.64 Fe4 S4 [S]12...
UNX X:804;
Invalid;
none;
submit data n/a n/a X n/a
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2IV2 2.27 Å EC: 1.2.1.2 REINTERPRETATION OF REDUCED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI ESCHERICHIA COLI OXIDOREDUCTASE 4FE-4S NAEROBIC COMPLETE PROTEOME DEHYDROGENASE DIRECT PROTEIN SEQUENCING FE4S4 FORMATE IRON IRON SULFUR CLUSTER IRON-SULFUR METAL-BINDING MGD MOLYBDENUM MOLYBDOPTERIN MOLYBDOPTERIN GUANINE DINUCLEOTIDE MPT NAD SECYS SELENIUM SELENOCYSTEINE
Ref.: FORMATE-REDUCED E. COLI FORMATE DEHYDROGENASE H: THE REINTERPRETATION OF THE CRYSTAL STRUCTURE SUGGESTS A NEW REACTION MECHANISM. J.BIOL.INORG.CHEM. V. 11 849 2006
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2IV2 - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2IV2 - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2IV2 - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 2MD; Similar ligands found: 81
No: Ligand ECFP6 Tc MDL keys Tc
1 2MD 1 1
2 MGD 0.694215 1
3 G1R 0.654206 0.880952
4 GP3 0.653846 0.892857
5 GSP 0.633027 0.894118
6 GDP 0.632075 0.891566
7 GTP 0.62963 0.891566
8 GNH 0.626168 0.880952
9 GCP 0.609091 0.870588
10 G2R 0.605263 0.860465
11 GNP 0.603604 0.870588
12 Y9Z 0.59322 0.813187
13 GMV 0.585586 0.870588
14 G 0.584906 0.879518
15 5GP 0.584906 0.879518
16 GFB 0.575 0.882353
17 GDR 0.575 0.882353
18 MD1 0.571429 0.97619
19 PGD O 0.57037 0.954023
20 G3A 0.570248 0.892857
21 GDD 0.566667 0.882353
22 GDC 0.566667 0.882353
23 GKE 0.566667 0.882353
24 G5P 0.565574 0.892857
25 GAV 0.565217 0.904762
26 GTG 0.561983 0.862069
27 GPG 0.559322 0.882353
28 GP2 0.558559 0.860465
29 6CK 0.557377 0.862069
30 GDP MG 0.548673 0.827586
31 JB2 0.548387 0.882353
32 GKD 0.548387 0.882353
33 G2P 0.547826 0.860465
34 JB3 0.546875 0.872093
35 GDX 0.544 0.892857
36 GPD 0.544 0.852273
37 GDP BEF 0.54386 0.808989
38 NGD 0.542636 0.882353
39 PGD 0.536765 0.963855
40 YGP 0.532787 0.895349
41 ALF 5GP 0.530435 0.8
42 GTP MG 0.529915 0.827586
43 BEF GDP 0.529915 0.8
44 GDP AF3 0.529412 0.8
45 GCP G 0.525424 0.837209
46 GDP ALF 0.516667 0.8
47 G G 0.516393 0.858824
48 ZGP 0.515152 0.844444
49 G3D 0.508475 0.879518
50 U2G 0.507576 0.905882
51 CAG 0.507353 0.815217
52 FEG 0.496241 0.813187
53 0O2 0.495935 0.879518
54 G4P 0.487603 0.879518
55 TPG 0.485915 0.879121
56 GMP 0.481132 0.785714
57 GDP 7MG 0.48062 0.83908
58 CG2 0.477941 0.905882
59 DBG 0.475524 0.872093
60 G4M 0.473333 0.815217
61 3GP 0.469027 0.845238
62 G1R G1R 0.465278 0.850575
63 FE9 0.464789 0.852632
64 I2C FE2 CMO CMO 0.450704 0.827957
65 G A A A 0.45 0.848837
66 U A G G 0.446809 0.858824
67 G G U 0.443609 0.858824
68 GH3 0.443548 0.869048
69 GPX 0.436508 0.845238
70 2GP 0.431034 0.857143
71 G1G 0.427586 0.852273
72 DGT 0.427419 0.827586
73 DGI 0.418033 0.827586
74 IDP 0.413223 0.86747
75 P2G 0.411765 0.790698
76 BGO 0.411348 0.850575
77 G C 0.402778 0.872093
78 GGM 0.402778 0.831461
79 U G A 0.402516 0.862069
80 MGP 0.4 0.860465
81 G2Q 0.4 0.860465
Ligand no: 2; Ligand: MGD; Similar ligands found: 78
No: Ligand ECFP6 Tc MDL keys Tc
1 MGD 1 1
2 PGD O 0.706349 0.954023
3 2MD 0.694215 1
4 G1R 0.636364 0.880952
5 GP3 0.635514 0.892857
6 GNH 0.623853 0.880952
7 GSP 0.616071 0.894118
8 GDP 0.614679 0.891566
9 GTP 0.612613 0.891566
10 PGD 0.606061 0.963855
11 GCP 0.59292 0.870588
12 G2R 0.589744 0.860465
13 GNP 0.587719 0.870588
14 GMV 0.584071 0.870588
15 Y9Z 0.578512 0.813187
16 G 0.568807 0.879518
17 5GP 0.568807 0.879518
18 GFB 0.560976 0.882353
19 GDR 0.560976 0.882353
20 G3A 0.556452 0.892857
21 GKE 0.552846 0.882353
22 GDC 0.552846 0.882353
23 GDD 0.552846 0.882353
24 G5P 0.552 0.892857
25 GAV 0.550847 0.904762
26 GTG 0.548387 0.862069
27 GKD 0.547619 0.882353
28 MD1 0.547445 0.97619
29 6CK 0.544 0.862069
30 GP2 0.54386 0.860465
31 NGD 0.541985 0.882353
32 MTE 0.541284 0.855422
33 JB2 0.535433 0.882353
34 GDP MG 0.534483 0.827586
35 G2P 0.533898 0.860465
36 GPG 0.532787 0.882353
37 YGP 0.532258 0.895349
38 GDX 0.53125 0.892857
39 GPD 0.53125 0.852273
40 GDP BEF 0.529915 0.808989
41 BEF GDP 0.529412 0.8
42 GCP G 0.525 0.837209
43 JB3 0.522727 0.872093
44 FEG 0.518797 0.813187
45 ALF 5GP 0.516949 0.8
46 GTP MG 0.516667 0.827586
47 ZGP 0.514925 0.844444
48 CAG 0.507246 0.815217
49 GDP ALF 0.504065 0.8
50 GDP AF3 0.504065 0.8
51 PTE 0.503937 0.827586
52 U2G 0.496296 0.905882
53 G3D 0.495868 0.879518
54 G G 0.492063 0.858824
55 0O2 0.484127 0.879518
56 CG2 0.478261 0.905882
57 TPG 0.475862 0.879121
58 G4P 0.475806 0.879518
59 GDP 7MG 0.469697 0.83908
60 GMP 0.46789 0.785714
61 DBG 0.465753 0.872093
62 3GP 0.456897 0.845238
63 FE9 0.455172 0.852632
64 G1R G1R 0.445946 0.850575
65 G1G 0.438356 0.852273
66 G4M 0.435897 0.815217
67 G G U 0.433824 0.858824
68 GH3 0.433071 0.869048
69 I2C FE2 CMO CMO 0.431507 0.827957
70 G A A A 0.430556 0.848837
71 U A G G 0.427586 0.858824
72 DGT 0.417323 0.827586
73 GPX 0.415385 0.845238
74 2GP 0.408333 0.857143
75 DGI 0.408 0.827586
76 IDP 0.403226 0.86747
77 BGO 0.402778 0.850575
78 P2G 0.401639 0.790698
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2IV2; Ligand: MGD; Similar sites found: 145
This union binding pocket(no: 1) in the query (biounit: 2iv2.bio1) has 37 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3G5K BB2 0.01461 0.41796 1.0929
2 2ZWA SAH 0.01328 0.40125 1.43885
3 2CHN NGT 0.03164 0.40128 1.53846
4 5MRH Q9Z 0.04508 0.40358 1.58046
5 3VC1 SAH 0.007097 0.41029 1.60256
6 3TLJ SAH 0.01133 0.40155 1.60858
7 3H8V ATP 0.01402 0.40886 1.71233
8 4C4A SAH 0.01007 0.41239 1.7341
9 4WNP 3RJ 0.03016 0.40565 1.74216
10 1Q11 TYE 0.03075 0.4165 1.88172
11 1ZGA SAH 0.02339 0.40782 1.96078
12 1KPG SAH 0.002081 0.43644 2.09059
13 4KRI SAH 0.001431 0.44711 2.30947
14 3EF0 ALF 0.02924 0.4226 2.68817
15 2EG5 SAH 0.0303 0.40222 2.68817
16 1JQD SAH 0.00479 0.40415 2.73973
17 2Q28 ADP 0.0005704 0.46894 2.83688
18 1KYQ NAD 0.02432 0.40065 2.91971
19 1XK5 TPG 0.005771 0.46254 2.94118
20 2YX1 SFG 0.009636 0.4269 2.97619
21 2ZIF SAM 0.01858 0.40026 3.0303
22 3P2E SAH 0.00357 0.42946 3.11111
23 2FK8 SAM 0.002127 0.43946 3.14465
24 2OBM ADP 0.03843 0.41325 3.17003
25 4DCM SAM 0.02734 0.40125 3.2
26 3G89 SAM 0.009698 0.42676 3.21285
27 2PXX SAH 0.01622 0.40296 3.25581
28 1PNO NAP 0.0007087 0.4043 3.33333
29 4C2C ALA ALA ALA 0.009662 0.43583 3.36323
30 5MGZ SAH 0.005086 0.42587 3.38983
31 1XDS SAM 0.01131 0.42347 3.47594
32 5KAX RHQ 0.003034 0.47117 3.61446
33 1QAN SAH 0.003848 0.42478 3.68852
34 3FUU ADN 0.004249 0.42942 3.69004
35 5GM1 SAH 0.006244 0.41268 3.7037
36 4NEC SAH 0.01806 0.41002 3.78788
37 2DVZ GLU 0.04091 0.40225 4.14013
38 1HFU NAG NDG 0.01362 0.41445 4.17495
39 1IG3 VIB 0.01033 0.45137 4.18251
40 4Y8D 49J 0.04776 0.40597 4.28571
41 1C4Q GLA GAL BGC 0.02869 0.40676 4.34783
42 2AL2 2PG 0.03773 0.40068 4.3578
43 2OOR TXP 0.0009156 0.43539 4.42708
44 1IM8 SAI 0.01227 0.40556 4.5082
45 3GDH SAH 0.01114 0.40187 4.56432
46 3GU3 SAH 0.01261 0.42887 4.57746
47 1RL4 BRR 0.03546 0.40918 4.78723
48 1L1E SAH 0.001615 0.44478 4.87805
49 1G55 SAH 0.007535 0.41812 4.95627
50 3FZG SAM 0.01012 0.42219 5
51 3BGD SAH 0.009476 0.40489 5
52 4K30 NLG 0.0434 0.40446 5
53 4FFG 0U8 0.03775 0.40456 5.0813
54 4MUQ 2D8 0.0231 0.41155 5.09804
55 4RDH AMP 0.007822 0.4276 5.20833
56 1LVL NAD 0.01579 0.40065 5.24017
57 2IZ1 ATR 0.04166 0.40929 5.27426
58 4IF4 BEF 0.02163 0.4276 5.28846
59 4MN7 SME 0.02747 0.4113 5.36913
60 4POS NAG SIA GAL 0.04065 0.4024 5.39568
61 1R27 MGD 0.0009273 0.41381 5.45455
62 4M6T SAM 0.03005 0.41197 5.46448
63 1GPM AMP 0.04766 0.40587 5.52381
64 2BZG SAH 0.005039 0.42948 5.60345
65 3AB4 THR 0.02749 0.4151 5.61798
66 2DTJ THR 0.02957 0.40963 5.61798
67 5N53 8NB 0.04577 0.40788 5.64103
68 2VN9 GVD 0.04119 0.40569 5.64784
69 5X62 SAH 0.004877 0.43373 5.66502
70 4A6D SAM 0.004307 0.42915 5.66572
71 3G2O SAM 0.01079 0.41414 5.68562
72 5EK3 5PK 0.02118 0.42114 5.7072
73 3RKR NAP 0.02443 0.41032 5.72519
74 1TE2 PGA 0.02847 0.42269 5.75221
75 1DJL NAP 0.001812 0.4105 5.7971
76 2Y2B AH0 0.01817 0.42873 5.88235
77 1G27 BB1 0.006594 0.42406 5.95238
78 5DA3 58V 0.02698 0.41171 6.03774
79 4RL4 PPV 0.02083 0.42476 6.13208
80 3ITA AIC 0.009898 0.43497 6.25
81 3H9R TAK 0.03346 0.41053 6.42202
82 1PL6 NAD 0.01513 0.40149 6.46067
83 1D4O NAP 0.0004088 0.45269 6.52174
84 3LST SAH 0.02421 0.40707 6.6092
85 4MA6 28E 0.01414 0.43493 7.00637
86 1N2X SAM 0.004209 0.42003 7.30897
87 4QTU SAM 0.0009771 0.45835 7.40741
88 1X8X TYR 0.02683 0.41184 7.45342
89 4OBW SAM 0.008932 0.41796 7.7821
90 4II2 ATP 0.00973 0.41006 7.97546
91 1ZQ9 SAM 0.007094 0.42259 8.42105
92 5KQG 6VX 0.02607 0.41249 8.42697
93 3H0L ADP 0.02859 0.4104 8.51064
94 2OX9 GAL NAG FUC 0.01404 0.42463 8.57143
95 3DXY SAM 0.0168 0.41858 8.7156
96 3EGI ADP 0.008633 0.44657 8.73786
97 4DR9 BB2 0.005135 0.43643 8.85417
98 2VDV SAM 0.009044 0.42826 8.94309
99 1LQY BB2 0.006756 0.42704 9.23913
100 2PHF MAN MAN BMA MAN 0.04764 0.40228 9.92064
101 2PHR MAN MAN BMA MAN 0.04945 0.40141 9.92064
102 5HJM MTA 0.01687 0.40218 10.5114
103 1JG3 ADN 0.006086 0.42568 10.6383
104 4I5I NAD 0.00623 0.40209 10.8014
105 3A4T SFG 0.01288 0.40183 10.9489
106 1KJ1 MAN 0.03376 0.4088 11.0092
107 3U31 NAD 0.0003718 0.46906 11.3793
108 3N7S 3N7 0.04148 0.40988 11.4583
109 2Z6D FMN 0.01861 0.40314 11.5385
110 3A25 SAM 0.006856 0.42328 11.9601
111 3PA8 621 0.0207 0.42591 12.2047
112 4FOU C2E 0.01633 0.4192 12.8205
113 2QQC AG2 0.02061 0.42738 13.2075
114 2BOS GLA GAL GLC NBU 0.04792 0.4085 13.2353
115 1N13 AG2 0.01662 0.43276 13.4615
116 1LSS NAD 0.01031 0.40893 13.5714
117 1M2K APR 0.0002655 0.45686 14.0562
118 3A27 SAM 0.009092 0.4176 14.3382
119 2CYC TYR 0.04927 0.40537 14.4
120 3I53 SAH 0.009698 0.41012 14.759
121 1L5Y BEF 0.02388 0.41825 15.4839
122 2IVF MGD 0.00000003534 0.55681 16.3636
123 2IVF MD1 0.0006311 0.42475 16.3636
124 3FGZ BEF 0.005001 0.4559 16.4062
125 2FKA BEF 0.01727 0.43535 17.0543
126 4MPO AMP 0.02163 0.42305 17.6471
127 3QMN A3P 0.04713 0.40623 18.6047
128 1Y63 ADP 0.0407 0.40237 19.5652
129 2NXE SAM 0.01772 0.40412 24.8032
130 3EGV SAH 0.02187 0.40285 24.8032
131 4YDD MD1 0.000000001072 0.67236 26.993
132 4YDD MGD 0.000000001072 0.67236 26.993
133 4KXQ APR 0.007586 0.4119 30
134 2VPY MGD 0.00000002345 0.46015 32.8671
135 1G8K MGD 0.00000000003471 0.50655 34.6853
136 1H0H MGD 0.000000000007849 0.69812 36.3636
137 1H0H 2MD 0.0006902 0.43142 36.3636
138 5E8J SAH 0.01258 0.42118 38.6364
139 1TMO 2MD 0.000001089 0.51158 40.5594
140 1DMR PGD 0.000007548 0.51963 40.8392
141 1EU1 MGD 0.000001324 0.50835 42.0979
142 2E7Z MGD 0.00000002436 0.57997 43.9161
143 3ML1 MGD 0.0000000006752 0.67897 46.014
144 2NYA MGD 0.000663 0.40829 46.5734
145 2V3V MGD 0.00000000001223 0.74775 48.6713
Pocket No.: 2; Query (leader) PDB : 2IV2; Ligand: 2MD; Similar sites found: 76
This union binding pocket(no: 2) in the query (biounit: 2iv2.bio1) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4J6C STR 0.03617 0.40741 1.46341
2 3R75 PYR 0.03989 0.40897 1.55039
3 3B6R CRN 0.03605 0.41072 1.5748
4 1KPG SAH 0.00208 0.43019 2.09059
5 1V6A TRE 0.009673 0.44062 2.10843
6 4KRI SAH 0.006543 0.4119 2.30947
7 3DMH SAM 0.01045 0.40299 2.3622
8 4WCX MET 0.02852 0.4099 2.5
9 4WCX ALA 0.02792 0.40676 2.5
10 1W62 PYC 0.04612 0.40168 2.657
11 2Q28 ADP 0.0007945 0.45581 2.83688
12 3NJ4 NAD 0.03013 0.40644 2.98851
13 1UJ5 5RP 0.01526 0.41516 3.0837
14 3P2E SAH 0.008066 0.40792 3.11111
15 2FK8 SAM 0.004526 0.41889 3.14465
16 1P31 EPU 0.005698 0.42111 3.15789
17 1H3F TYE 0.02592 0.41829 3.24074
18 5M67 ADE 0.004495 0.41201 3.54906
19 5M67 3D1 0.004844 0.41072 3.54906
20 5M67 NAD 0.004855 0.41068 3.54906
21 1BW9 PPY 0.01162 0.41724 3.65169
22 5GM1 SAH 0.006361 0.40647 3.7037
23 2CYB TYR 0.04214 0.40291 3.71517
24 4NEC SAH 0.007557 0.42253 3.78788
25 1KYZ SAH 0.01276 0.40516 3.83562
26 3E7W AMP 0.01845 0.40748 4.10959
27 4S00 AKR 0.04386 0.40237 4.47427
28 3LGS SAH 0.00969 0.42496 4.49438
29 1LOJ U 0.02638 0.40296 4.5977
30 2ZX2 RAM 0.04384 0.40534 4.61538
31 1L1E SAH 0.006645 0.4116 4.87805
32 3GXA MET 0.03827 0.4022 5.09091
33 2GZM DGL 0.02805 0.40932 5.24345
34 2IZ1 ATR 0.02995 0.41395 5.27426
35 4IF4 BEF 0.00152 0.48534 5.28846
36 1R27 MGD 0.000008669 0.50371 5.45455
37 5N53 8NB 0.005957 0.45183 5.64103
38 5EK3 5PK 0.01628 0.4217 5.7072
39 3IR1 MET 0.03617 0.4035 5.71429
40 3RKR NAP 0.0217 0.41122 5.72519
41 1TE2 PGA 0.01025 0.44024 5.75221
42 2CBZ ATP 0.03094 0.41047 5.90717
43 4G4P GLN 0.02894 0.41265 6.14754
44 3LST SAH 0.02441 0.40497 6.6092
45 1XMU ROF 0.0252 0.40085 7.03518
46 4QTU SAM 0.01224 0.40292 7.40741
47 1ZQ9 SAM 0.008876 0.41235 8.42105
48 2XUA SHF 0.04804 0.40039 8.64662
49 3EGI ADP 0.007007 0.44566 8.73786
50 3BQF SSM 0.01364 0.4103 9.27835
51 4Q3F TLA 0.04153 0.40317 9.40171
52 4QAR ADE 0.02177 0.40397 9.45274
53 2ZQO NGA 0.04249 0.40319 10
54 1ZOS MTM 0.01127 0.41429 10.4348
55 1JG3 ADN 0.001675 0.44525 10.6383
56 3U31 NAD 0.002019 0.43074 11.3793
57 3PA8 621 0.04731 0.40108 12.2047
58 3OND ADN 0.006658 0.4044 12.9098
59 1LSS NAD 0.0114 0.40134 13.5714
60 1M2K APR 0.003603 0.40554 14.0562
61 4CCN OGA 0.03082 0.41133 14.2857
62 2CYC TYR 0.02613 0.41636 14.4
63 2IVF MD1 0.000001358 0.50658 16.3636
64 2FKA BEF 0.01625 0.44082 17.0543
65 1JL0 PUT 0.02792 0.40748 20.0599
66 4YDD MD1 0.0001708 0.48526 26.993
67 4YDD MGD 0.0001708 0.48526 26.993
68 1G8K MGD 0.0004323 0.40809 34.6853
69 1H0H 2MD 0.000002594 0.51495 36.3636
70 1H0H MGD 0.0002409 0.41943 36.3636
71 1DMR PGD 0.00007249 0.49767 40.8392
72 1EU1 MGD 0.0004251 0.40729 42.0979
73 2E7Z MGD 0.001151 0.40107 43.9161
74 3ML1 MGD 0.000002468 0.56096 46.014
75 2NYA MGD 0.000000482 0.49738 46.5734
76 2V3V MGD 0.00000106 0.57711 48.6713
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