Receptor
PDB id Resolution Class Description Source Keywords
2P4T 1.15 Å EC: 1.5.1.3 STRUCTURE OF THE Q67H MUTANT OF R67 DIHYDROFOLATE REDUCTASE- NADP+ COMPLEX REVEALS A NOVEL COFACTOR BINDING MODE ESCHERICHIA COLI BACTERIAL INFECTIONS CRYSTAL STRUCTURE FOLATE METABOLISM NADP+ R67 DHFR SYMMETRIC BINDING TRIMETHOPRIM-RESISTANCEOXIDOREDUCTASE
Ref.: STRUCTURE OF THE Q67H MUTANT OF R67 DIHYDROFOLATE REDUCTASE-NADP+ COMPLEX REVEALS A NOVEL COFACTOR BINDING MODE. PROTEIN SCI. V. 16 1063 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAP A:157;
Valid;
none;
Kd = 0.027 uM
743.405 C21 H28 N7 O17 P3 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2P4T 1.15 Å EC: 1.5.1.3 STRUCTURE OF THE Q67H MUTANT OF R67 DIHYDROFOLATE REDUCTASE- NADP+ COMPLEX REVEALS A NOVEL COFACTOR BINDING MODE ESCHERICHIA COLI BACTERIAL INFECTIONS CRYSTAL STRUCTURE FOLATE METABOLISM NADP+ R67 DHFR SYMMETRIC BINDING TRIMETHOPRIM-RESISTANCEOXIDOREDUCTASE
Ref.: STRUCTURE OF THE Q67H MUTANT OF R67 DIHYDROFOLATE REDUCTASE-NADP+ COMPLEX REVEALS A NOVEL COFACTOR BINDING MODE. PROTEIN SCI. V. 16 1063 2007
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 2RK2 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
2 1VIF - FOL C19 H19 N7 O6 c1cc(ccc1C....
3 2RK1 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 2P4T Kd = 0.027 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 2RK2 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
2 1VIF - FOL C19 H19 N7 O6 c1cc(ccc1C....
3 2RK1 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 2P4T Kd = 0.027 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 2RK2 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
2 1VIF - FOL C19 H19 N7 O6 c1cc(ccc1C....
3 2RK1 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 2P4T Kd = 0.027 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAP; Similar ligands found: 127
No: Ligand ECFP6 Tc MDL keys Tc
1 NAP 1 1
2 NA0 0.881356 0.986301
3 TAP 0.872881 0.934211
4 NDO 0.840336 0.972603
5 NAD 0.811966 0.986111
6 N01 0.733871 0.958904
7 A3D 0.712 0.972603
8 NBP 0.707692 0.935065
9 NAD IBO 0.688 0.921053
10 NHD 0.68254 0.958904
11 NJP 0.661417 0.972973
12 NAJ PYZ 0.659091 0.898734
13 NFD 0.658915 0.934211
14 DND 0.619048 0.959459
15 NXX 0.619048 0.959459
16 ZID 0.605839 0.972603
17 NAQ 0.59854 0.922078
18 ATR 0.59292 0.917808
19 NAE 0.591241 0.946667
20 NDE 0.58042 0.986301
21 A22 0.571429 0.958904
22 AMP NAD 0.571429 0.933333
23 NAJ 0.567164 0.986111
24 A2R 0.563025 0.932432
25 NDC 0.561644 0.922078
26 NA7 0.552846 0.907895
27 ODP 0.551471 0.935065
28 A2P 0.539823 0.930556
29 8ID 0.537313 0.910256
30 NAD BBN 0.525974 0.865854
31 NPW 0.525547 0.8875
32 CNA 0.521739 0.959459
33 NZQ 0.521739 0.910256
34 NAD CJ3 0.519231 0.835294
35 NDP 0.514493 0.922078
36 PO4 PO4 A A A A PO4 0.503937 0.930556
37 DG1 0.503401 0.922078
38 1DG 0.503401 0.922078
39 NAD TDB 0.5 0.696078
40 TXP 0.5 0.922078
41 NMN AMP PO4 0.492958 0.921053
42 XNP 0.492958 0.875
43 25L 0.492308 0.958904
44 25A 0.492063 0.972222
45 NAD NDT 0.490909 0.747368
46 NMN 0.486726 0.888889
47 NGD 0.485714 0.935065
48 2AM 0.477876 0.891892
49 ADP 0.458333 0.945205
50 PAP 0.451613 0.931507
51 ADP MG 0.45082 0.906667
52 BEF ADP 0.447154 0.883117
53 ADP BEF 0.447154 0.883117
54 A2D 0.445378 0.945205
55 AN2 0.442623 0.932432
56 ADP PO3 0.44 0.944444
57 SAP 0.44 0.896104
58 AGS 0.44 0.896104
59 M33 0.439024 0.906667
60 AR6 AR6 0.438849 0.945205
61 BA3 0.438017 0.945205
62 ATP MG 0.436508 0.906667
63 ADP BMA 0.43609 0.92
64 OAD 0.43609 0.92
65 ATP 0.435484 0.945205
66 OOB 0.435115 0.958904
67 B4P 0.434426 0.945205
68 AP5 0.434426 0.945205
69 GAP 0.433071 0.92
70 0WD 0.432432 0.922078
71 5FA 0.432 0.945205
72 2A5 0.432 0.87013
73 AQP 0.432 0.945205
74 00A 0.428571 0.909091
75 CA0 0.427419 0.92
76 ALF ADP 0.426357 0.871795
77 ADP ALF 0.426357 0.871795
78 ACP 0.424 0.92
79 NAJ PZO 0.423841 0.897436
80 9SN 0.423358 0.897436
81 VO4 ADP 0.423077 0.932432
82 ANP MG 0.423077 0.896104
83 ADP VO4 0.423077 0.932432
84 WAQ 0.422222 0.884615
85 ACQ 0.421875 0.92
86 V3L 0.421875 0.945205
87 ADQ 0.421053 0.92
88 AR6 0.420635 0.918919
89 APR 0.420635 0.918919
90 ATP A A A 0.42029 0.958333
91 CO7 0.419753 0.786517
92 1ZZ 0.419118 0.841463
93 3OD 0.419118 0.92
94 DLL 0.41791 0.958904
95 AD9 0.417323 0.92
96 NAX 0.416667 0.875
97 OVE 0.416667 0.857143
98 MYR AMP 0.416058 0.841463
99 AV2 0.415385 0.868421
100 A3P 0.414634 0.944444
101 NNR 0.414414 0.72973
102 ALF ADP 3PG 0.413793 0.8625
103 OMR 0.413793 0.831325
104 LA8 ALF 3PG 0.413793 0.8625
105 ANP 0.410853 0.92
106 A1R 0.410448 0.860759
107 ABM 0.409836 0.893333
108 AMP 0.408333 0.944444
109 A 0.408333 0.944444
110 SON 0.408 0.933333
111 PPS 0.407692 0.829268
112 5AL 0.407692 0.932432
113 TYR AMP 0.407143 0.933333
114 NAI 0.406897 0.909091
115 7D3 0.406504 0.857143
116 DAL AMP 0.406015 0.932432
117 ADX 0.404762 0.829268
118 ATF 0.40458 0.907895
119 3UK 0.404412 0.945946
120 AMP DBH 0.404255 0.894737
121 139 0.402685 0.875
122 AMP MG 0.401639 0.893333
123 50T 0.401575 0.906667
124 SRP 0.401515 0.907895
125 A A 0.40146 0.972222
126 FA5 0.4 0.933333
127 3AM 0.4 0.90411
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2P4T; Ligand: NAP; Similar sites found: 166
This union binding pocket(no: 1) in the query (biounit: 2p4t.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1JOT GAL A2G 0.000009091 0.53401 None
2 1NME 159 0.000007185 0.52308 None
3 4NYT PC 0.0004245 0.49239 None
4 1C3M MAN MAN 0.00004547 0.49191 None
5 1XX4 BAM 0.0002964 0.4882 None
6 3QDY CBS 0.001647 0.47204 None
7 4AP9 1PS 0.00004018 0.47112 None
8 3I8T LBT 0.0007814 0.46624 None
9 4A6F SEP 0.007271 0.46314 None
10 1JGS SAL 0.0114 0.46131 None
11 1NXJ TLA 0.0002157 0.45761 None
12 3B9Z CO2 0.002626 0.45535 None
13 4RJK PYR 0.01769 0.45033 None
14 3QDW A2G 0.009986 0.44762 None
15 1NPL MAN 0.003927 0.44716 None
16 2GN2 C5P 0.0004503 0.44329 None
17 3KPE TM3 0.004779 0.44317 None
18 1HFA PIO 0.01153 0.43812 None
19 1QB7 ADE 0.002109 0.43657 None
20 3NOJ PYR 0.004418 0.43599 None
21 2WL9 MBD 0.0001404 0.4348 None
22 3S9K CIT 0.03124 0.43425 None
23 1PTR PRB 0.009915 0.43419 None
24 1JAC AMG 0.02657 0.43219 None
25 1TV5 N8E 0.0006884 0.43209 None
26 3UEC ALA ARG TPO LYS 0.01298 0.42849 None
27 1A5V Y3 0.008952 0.4249 None
28 1UGX GAL MGC 0.00009917 0.42436 None
29 3VPD CIT 0.03721 0.42407 None
30 3QDT A2G GAL 0.02161 0.42351 None
31 3QDV A2G 0.03097 0.42166 None
32 1TUV VK3 0.03239 0.42063 None
33 2Q37 3AL 0.01122 0.42045 None
34 3WUD GLC GAL 0.02501 0.42028 None
35 3LTW HLZ 0.01664 0.41772 None
36 4PNO U5P 0.00382 0.41701 None
37 2X2T GAL NGA 0.03794 0.41697 None
38 1UW1 ADP 0.01377 0.4164 None
39 1MVQ MMA 0.0001261 0.4146 None
40 1O51 ADP 0.0004992 0.41377 None
41 1WTC ACP 0.02821 0.412 None
42 1Q3P GLU ALA GLN THR ARG LEU 0.01059 0.41197 None
43 1J2Z SOG 0.00368 0.41156 None
44 4PB2 5UD 0.002999 0.40912 None
45 3QDV NDG 0.0361 0.40674 None
46 2W24 LYS 0.0004019 0.40672 None
47 1ZUW DGL 0.01462 0.40599 None
48 3M6P BB2 0.01265 0.40504 None
49 1MZV AMP 0.01293 0.40405 None
50 1UFY MLI 0.03375 0.40319 None
51 2OFE NAG 0.01536 0.40197 None
52 2WBV SIA 0.02658 0.40087 None
53 4B16 NAG 0.001116 0.50764 3.22581
54 4Q3F TLA 0.0003122 0.49861 3.22581
55 2WGC SIA GAL BGC 0.01595 0.45292 3.22581
56 1C1L GAL BGC 0.0118 0.43051 3.22581
57 1O9U ADZ 0.04467 0.41318 3.22581
58 4Q3R XA2 0.0007294 0.40866 3.22581
59 2NZ2 ASP 0.00001423 0.54238 4.83871
60 3IHB TRS 0.001454 0.48401 4.83871
61 3PHQ KDO 0.01003 0.47349 4.83871
62 3K3G MMU 0.0007456 0.47039 4.83871
63 4JCA CIT 0.02722 0.4316 4.83871
64 2Q8M AMP 0.003069 0.42516 4.83871
65 1NU4 MLA 0.005688 0.42347 4.83871
66 2BMK PDD 0.01512 0.42241 4.83871
67 3MD0 GDP 0.009418 0.41414 4.83871
68 3R51 MMA 0.04552 0.41274 4.83871
69 2OWZ CIT 0.02258 0.41146 4.83871
70 2BVE PH5 0.01173 0.40822 4.83871
71 2VDJ HSE 0.0485 0.40555 4.83871
72 3BY8 MLT 0.04113 0.40394 4.83871
73 1A5Z OXM 0.0004934 0.50626 6.45161
74 3UBW 6SP 0.03431 0.44101 6.45161
75 1A5Z FBP 0.0003535 0.43804 6.45161
76 3F81 STT 0.03976 0.41588 6.45161
77 2R00 OEG 0.0261 0.41367 6.45161
78 2BLE 5GP 0.001281 0.413 6.45161
79 1NML CIT 0.01385 0.41147 6.45161
80 2J0B UDP 0.01276 0.40988 6.45161
81 3I7S PYR 0.04149 0.40904 6.45161
82 1GZF ADP 0.01223 0.40574 6.45161
83 1ML4 PAL 0.003196 0.4028 6.45161
84 1GZF NAD 0.01672 0.4028 6.45161
85 3GD8 BOG 0.000006658 0.60027 8.06452
86 2VMD MBG 0.0002882 0.52827 8.06452
87 3O03 GCO 0.00001039 0.51686 8.06452
88 4M7F BM3 0.00007689 0.51032 8.06452
89 1LTH FBP 0.0003399 0.49688 8.06452
90 1BTN I3P 0.004291 0.49363 8.06452
91 1LTH OXM 0.0003972 0.46645 8.06452
92 1SOW OXL 0.00705 0.45556 8.06452
93 1RYI GOA 0.02067 0.45319 8.06452
94 3EJ0 11X 0.002083 0.45053 8.06452
95 2BZ1 TAU 0.0183 0.44948 8.06452
96 4ODV GP1 Z9M 0.01859 0.44908 8.06452
97 4E28 9MZ 0.005638 0.43981 8.06452
98 1Y7P RIP 0.01408 0.43295 8.06452
99 3FPZ AHZ 0.0009081 0.42868 8.06452
100 4E28 0MZ 0.009412 0.42391 8.06452
101 4C2C ALA ALA ALA 0.008468 0.42358 8.06452
102 4M51 BEZ 0.02498 0.42031 8.06452
103 1GJW GLC 0.03643 0.40654 8.06452
104 4TSK NDP 0.002747 0.40116 8.06452
105 3TKA CTN 0.002718 0.50896 9.67742
106 4WBD CIT 0.003707 0.4622 9.67742
107 1B74 DGN 0.01715 0.4286 9.67742
108 1Z45 GAL 0.01022 0.41729 9.67742
109 2WIC GNP 0.0006597 0.41518 9.67742
110 4U36 TNR 0.001056 0.40693 9.67742
111 4AF0 MOA 0.001128 0.40602 9.67742
112 1JH7 UVC 0.02552 0.40416 9.67742
113 1VCO GLN 0.0008049 0.4041 9.67742
114 1RN8 DUP 0.001526 0.40346 9.67742
115 3VHZ L2P GLC MAN SGA 0.003965 0.40208 9.67742
116 3JQM GTP 0.01887 0.40125 9.67742
117 3EYK EYK 0.00007965 0.52634 11.2903
118 3IB9 BTN 0.007505 0.44334 11.2903
119 3CL5 SIO 0.003679 0.43949 11.2903
120 1DXY COI 0.01805 0.43408 11.2903
121 1D3V ABH 0.0005573 0.41229 11.2903
122 2CWH PYC 0.03046 0.40588 11.2903
123 3VCA PRO 0.0216 0.40517 11.2903
124 2PNZ 5GP 0.01536 0.40507 11.2903
125 4G1V FAD 0.00005719 0.47627 12.9032
126 1FX8 BOG 0.0003351 0.44802 12.9032
127 1NF8 BOG 0.0105 0.43298 12.9032
128 2FGQ MLT 0.01456 0.42045 12.9032
129 1JA9 NDP 0.001159 0.42012 12.9032
130 1V5F FAD 0.0134 0.41034 12.9032
131 1V5F TPP 0.0134 0.41034 12.9032
132 3P3N AKG 0.03466 0.40264 12.9032
133 4F8L GAL 0.001626 0.50979 14.5161
134 4N69 SER 0.008647 0.43109 14.5161
135 3SJK LYS PRO VAL LEU ARG THR ALA 0.007742 0.42023 14.5161
136 3W8S GSH 0.01564 0.41388 14.5161
137 1HQL GLA MBG 0.04266 0.40315 14.5161
138 4IHQ ADP 0.01942 0.40071 14.5161
139 2ZWS PLM 0.00231 0.50106 16.129
140 2HVK TBA 0.0003036 0.49917 16.129
141 1LDM OXM 0.001186 0.44687 16.129
142 3OAZ 2M5 0.03057 0.43257 16.129
143 1KC7 PPR 0.01164 0.4308 16.129
144 2I4O ATP 0.01146 0.40622 16.129
145 3ZOD HQE 0.004329 0.44133 17.7419
146 3CL7 HYN 0.000001711 0.44435 19.3548
147 2XDQ MGX 0.04498 0.41302 19.3548
148 1QDS PGA 0.01356 0.40319 19.3548
149 4N02 FNR 0.000004251 0.48395 20.9677
150 4TMK T5A 0.001636 0.43306 20.9677
151 2JE7 XMM 0.0002367 0.42023 20.9677
152 1Y0L HAN 0.04127 0.4182 20.9677
153 3W2W ATP 0.005153 0.41613 20.9677
154 3B82 NAD 0.01851 0.40546 20.9677
155 4WVH ASP HIS ASP ALA HIS ALA 0.00164 0.44642 22.5806
156 1Q3Q ANP 0.00009478 0.44465 22.5806
157 1H2M OGA 0.03576 0.40199 23.0769
158 2V9M CIT 0.00001491 0.52516 24.1935
159 4DN8 BMA 0.006573 0.43668 24.1935
160 1JN2 SFP 0.0459 0.41589 24.1935
161 1Q72 COC 0.00776 0.42254 27.4194
162 5E65 5N6 GAL 0.004227 0.40931 27.4194
163 3VOZ 04A 0.0001034 0.46685 29.0323
164 2QIA U20 0.001675 0.40501 30.6452
165 1PEA ACM 0.0144 0.43246 35.4839
166 1QO0 BMD 0.02165 0.41233 35.4839
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