0.024390 0.000000 0.003298 0.000000 0.011161 0.000000 0.000000 0.000000 0.024257 0.00000 0.00000 0.00000 Allerston, C.K. Djordjevic, S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 97.70 90.00 41.000 89.600 41.600 C17 H19 N7 O5 S3 497.572 (S)-2-(3-(benzo[c][1,2,5]thiadiazole-4-sulfonamido)thiophene-2-carboxamido)-5-guanidinopentanoic acid (2S)-2-[[3-(2,1,3-benzothiadiazol-4-ylsulfonylamino)thiophen-2-yl]carbonylamino]-5-carbamimidamido-pentanoic acid non-polymer C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C3 H8 O3 92.094 GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL non-polymer C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N C N 2 N N N 3 N O N 4 S C N 5 N C N 6 N C N 7 N N N 8 N C N 9 N C N 10 N O N 11 N O N 12 N O Y 13 N C Y 14 N C Y 15 N C Y 16 N C Y 17 N C Y 18 N N Y 19 N N N 20 N N Y 21 N S Y 22 N S N 23 N C Y 24 N C Y 25 N C Y 26 N C Y 27 N C Y 28 N C N 29 N S N 30 N N N 31 N N N 32 N O N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N H N 42 N H N 43 N H N 44 N H N 45 N H N 46 N H N 47 N H N 48 N H N 49 N H N 50 N H N 51 N H N 52 N N N 53 S C N 54 N C N 55 N O N 56 N C N 57 N O N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N N N 66 S C N 67 N C N 68 N O N 69 N C N 70 N C N 71 N C N 72 N N N 73 N C N 74 N N N 75 N N N 76 N O N 77 N H N 78 N H N 79 N H N 80 N H N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N N N 93 S C N 94 N C N 95 N O N 96 N C N 97 N C N 98 N O N 99 N N N 100 N O N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N N N 110 S C N 111 N C N 112 N O N 113 N C N 114 N C N 115 N O N 116 N O N 117 N O N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N N N 126 R C N 127 N C N 128 N O N 129 N C N 130 N S N 131 N O N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N N N 140 S C N 141 N C N 142 N O N 143 N C N 144 N C N 145 N C N 146 N O N 147 N N N 148 N O N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N H N 159 N N N 160 S C N 161 N C N 162 N O N 163 N C N 164 N C N 165 N C N 166 N O N 167 N O N 168 N O N 169 N H N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N N N 179 N C N 180 N C N 181 N O N 182 N O N 183 N H N 184 N H N 185 N H N 186 N H N 187 N H N 188 N C N 189 N O N 190 N C N 191 N O N 192 N C N 193 N O N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N N N 203 S C N 204 N C N 205 N O N 206 N C Y 207 N C Y 208 N N Y 209 N C Y 210 N C Y 211 N N N 212 N O N 213 N H N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N O N 224 N H N 225 N H N 226 N N N 227 S C N 228 N C N 229 N O N 230 S C N 231 N C N 232 N C N 233 N C N 234 N O N 235 N H N 236 N H N 237 N H N 238 N H N 239 N H N 240 N H N 241 N H N 242 N H N 243 N H N 244 N H N 245 N H N 246 N H N 247 N H N 248 N N N 249 S C N 250 N C N 251 N O N 252 N C N 253 N C N 254 N C N 255 N C N 256 N O N 257 N H N 258 N H N 259 N H N 260 N H N 261 N H N 262 N H N 263 N H N 264 N H N 265 N H N 266 N H N 267 N H N 268 N H N 269 N H N 270 N N N 271 S C N 272 N C N 273 N O N 274 N C N 275 N C N 276 N C N 277 N C N 278 N N N 279 N O N 280 N H N 281 N H N 282 N H N 283 N H N 284 N H N 285 N H N 286 N H N 287 N H N 288 N H N 289 N H N 290 N H N 291 N H N 292 N H N 293 N H N 294 N H N 295 N N N 296 S C N 297 N C N 298 N O N 299 N C N 300 N C N 301 N S N 302 N C N 303 N O N 304 N H N 305 N H N 306 N H N 307 N H N 308 N H N 309 N H N 310 N H N 311 N H N 312 N H N 313 N H N 314 N H N 315 N N N 316 S C N 317 N C N 318 N O N 319 N C Y 320 N C Y 321 N C Y 322 N C Y 323 N C Y 324 N C Y 325 N C N 326 N O N 327 N H N 328 N H N 329 N H N 330 N H N 331 N H N 332 N H N 333 N H N 334 N H N 335 N H N 336 N H N 337 N H N 338 N N N 339 S C N 340 N C N 341 N O N 342 N C N 343 N C N 344 N C N 345 N O N 346 N H N 347 N H N 348 N H N 349 N H N 350 N H N 351 N H N 352 N H N 353 N H N 354 N H N 355 N N N 356 S C N 357 N C N 358 N O N 359 N C N 360 N O N 361 N O N 362 N H N 363 N H N 364 N H N 365 N H N 366 N H N 367 N H N 368 N H N 369 N N N 370 S C N 371 N C N 372 N O N 373 R C N 374 N O N 375 N C N 376 N O N 377 N H N 378 N H N 379 N H N 380 N H N 381 N H N 382 N H N 383 N H N 384 N H N 385 N H N 386 N N N 387 S C N 388 N C N 389 N O N 390 N C Y 391 N C Y 392 N C Y 393 N C Y 394 N N Y 395 N C Y 396 N C Y 397 N C Y 398 N C Y 399 N C N 400 N O N 401 N H N 402 N H N 403 N H N 404 N H N 405 N H N 406 N H N 407 N H N 408 N H N 409 N H N 410 N H N 411 N H N 412 N H N 413 N N N 414 S C N 415 N C N 416 N O N 417 N C Y 418 N C Y 419 N C Y 420 N C Y 421 N C Y 422 N C Y 423 N C N 424 N O N 425 N O N 426 N H N 427 N H N 428 N H N 429 N H N 430 N H N 431 N H N 432 N H N 433 N H N 434 N H N 435 N H N 436 N H N 437 N N N 438 S C N 439 N C N 440 N O N 441 N C N 442 N C N 443 N C N 444 N O N 445 N H N 446 N H N 447 N H N 448 N H N 449 N H N 450 N H N 451 N H N 452 N H N 453 N H N 454 N H N 455 N H N 1 N sing N 2 N doub N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N doub N 21 N sing N 22 N doub N 23 N doub N 24 N doub Y 25 N sing Y 26 N doub N 27 N sing Y 28 N sing Y 29 N doub N 30 N sing Y 31 N doub N 32 N sing Y 33 N sing N 34 N sing Y 35 N sing N 36 N sing Y 37 N doub Y 38 N sing Y 39 N doub Y 40 N sing N 41 N sing N 42 N sing N 43 N sing Y 44 N sing N 45 N sing Y 46 N doub N 47 N sing Y 48 N sing Y 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N doub N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N doub N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N doub N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N doub N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N doub N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N doub N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N doub N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N doub N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N doub N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N doub N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N doub N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N doub N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N doub N 202 N sing N 203 N sing N 204 N sing N 205 N sing Y 206 N sing Y 207 N doub Y 208 N doub N 209 N sing Y 210 N sing N 211 N sing Y 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N doub N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N doub N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N sing N 263 N sing N 264 N sing N 265 N sing N 266 N doub N 267 N sing N 268 N sing N 269 N sing N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N sing N 280 N sing N 281 N sing N 282 N sing N 283 N sing N 284 N sing N 285 N sing N 286 N sing N 287 N sing N 288 N sing N 289 N sing N 290 N doub N 291 N sing N 292 N sing N 293 N sing N 294 N sing N 295 N sing N 296 N sing N 297 N sing N 298 N sing N 299 N sing N 300 N sing N 301 N sing N 302 N sing N 303 N sing N 304 N sing N 305 N sing N 306 N sing N 307 N sing N 308 N sing N 309 N doub N 310 N sing N 311 N sing N 312 N sing N 313 N sing Y 314 N doub Y 315 N sing Y 316 N sing N 317 N sing Y 318 N doub N 319 N sing Y 320 N doub N 321 N sing Y 322 N sing N 323 N sing N 324 N sing N 325 N sing N 326 N sing N 327 N sing N 328 N sing N 329 N sing N 330 N sing N 331 N sing N 332 N doub N 333 N sing N 334 N sing N 335 N sing N 336 N sing N 337 N sing N 338 N sing N 339 N sing N 340 N sing N 341 N sing N 342 N sing N 343 N sing N 344 N sing N 345 N sing N 346 N sing N 347 N sing N 348 N sing N 349 N doub N 350 N sing N 351 N sing N 352 N sing N 353 N sing N 354 N sing N 355 N sing N 356 N sing N 357 N sing N 358 N sing N 359 N sing N 360 N sing N 361 N sing N 362 N doub N 363 N sing N 364 N sing N 365 N sing N 366 N sing N 367 N sing N 368 N sing N 369 N sing N 370 N sing N 371 N sing N 372 N sing N 373 N sing N 374 N sing N 375 N sing N 376 N sing N 377 N sing N 378 N doub N 379 N sing N 380 N sing N 381 N sing N 382 N sing Y 383 N doub Y 384 N sing Y 385 N sing N 386 N sing Y 387 N doub Y 388 N sing Y 389 N sing N 390 N sing Y 391 N sing Y 392 N doub N 393 N sing Y 394 N doub N 395 N sing Y 396 N sing N 397 N sing N 398 N sing N 399 N sing N 400 N sing N 401 N sing N 402 N sing N 403 N sing N 404 N sing N 405 N sing N 406 N doub N 407 N sing N 408 N sing N 409 N sing N 410 N sing Y 411 N doub Y 412 N sing Y 413 N sing N 414 N sing Y 415 N doub N 416 N sing Y 417 N doub N 418 N sing Y 419 N sing N 420 N sing N 421 N sing N 422 N sing N 423 N sing N 424 N sing N 425 N sing N 426 N sing N 427 N sing N 428 N sing N 429 N sing N 430 N doub N 431 N sing N 432 N sing N 433 N sing N 434 N sing N 435 N sing N 436 N sing N 437 N sing N 438 N sing N 439 N sing N 440 N sing N 441 N sing US J.Med.Chem. JMCMAR 0151 0022-2623 53 2215 2226 10.1021/jm901755g 20151671 Small molecule inhibitors of the neuropilin-1 vascular endothelial growth factor A (VEGF-A) interaction. 2010 10.2210/pdb3i97/pdb pdb_00003i97 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 OSMIC MIRRORS IMAGE PLATE 2008-05-01 RIGAKU RAXIS IV SINGLE WAVELENGTH M x-ray 1 1.54 1.0 1.54 ROTATING ANODE RIGAKU 17917.291 Neuropilin-1 domain B1, F5/8 type C 1 2 man polymer 497.572 (S)-2-(3-(benzo[c][1,2,5]thiadiazole-4-sulfonamido)thiophene-2-carboxamido)-5-guanidinopentanoic acid 2 syn non-polymer 92.094 GLYCEROL 1 syn non-polymer 18.015 water 8 nat water Vascular endothelial cell growth factor 165 receptor no no GHMFKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVDLGLLRFVTAVGTQGAISKET KKKYYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTDVVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKIT GHMFKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVDLGLLRFVTAVGTQGAISKET KKKYYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTDVVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKIT A,B polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n human sample NP1-B1, NRP, NRP1, VEGF165R 9606 Homo sapiens 562 Escherichia coli Rosetta 1 2.15 42.85 6 100 mM MES (pH 6.0), 10% PEG 8K and 200 mM Zn(AcO, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K 293.15 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_ncs_dom_lim struct_site repository Initial release Version format compliance Data collection Database references Derived calculations Refinement description 1 0 2010-03-02 1 1 2011-07-13 1 2 2023-09-06 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_ncs_dom_lim.beg_auth_comp_id _struct_ncs_dom_lim.beg_label_asym_id _struct_ncs_dom_lim.beg_label_comp_id _struct_ncs_dom_lim.beg_label_seq_id _struct_ncs_dom_lim.end_auth_comp_id _struct_ncs_dom_lim.end_label_asym_id _struct_ncs_dom_lim.end_label_comp_id _struct_ncs_dom_lim.end_label_seq_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2009-07-10 REL REL 8DR (S)-2-(3-(benzo[c][1,2,5]thiadiazole-4-sulfonamido)thiophene-2-carboxamido)-5-guanidinopentanoic acid GOL GLYCEROL HOH water 1KEX PDB ENTRY 1KEX PDB experimental model 8DR 156 2 8DR 8DR 156 A GOL 157 3 GOL GOL 157 A 8DR 156 2 8DR 8DR 156 B HOH 158 4 HOH HOH 158 A HOH 159 4 HOH HOH 159 A HOH 160 4 HOH HOH 160 A HOH 161 4 HOH HOH 161 A HOH 162 4 HOH HOH 162 A HOH 163 4 HOH HOH 163 A HOH 164 4 HOH HOH 164 A HOH 157 4 HOH HOH 157 B n 1 -2 A n 2 -1 A n 3 0 A n 4 1 A LYS 2 n 5 LYS 2 A CYS 3 n 6 CYS 3 A MET 4 n 7 MET 4 A GLU 5 n 8 GLU 5 A ALA 6 n 9 ALA 6 A LEU 7 n 10 LEU 7 A GLY 8 n 11 GLY 8 A MET 9 n 12 MET 9 A GLU 10 n 13 GLU 10 A SER 11 n 14 SER 11 A GLY 12 n 15 GLY 12 A GLU 13 n 16 GLU 13 A ILE 14 n 17 ILE 14 A HIS 15 n 18 HIS 15 A SER 16 n 19 SER 16 A ASP 17 n 20 ASP 17 A GLN 18 n 21 GLN 18 A ILE 19 n 22 ILE 19 A THR 20 n 23 THR 20 A ALA 21 n 24 ALA 21 A SER 22 n 25 SER 22 A SER 23 n 26 SER 23 A GLN 24 n 27 GLN 24 A TYR 25 n 28 TYR 25 A SER 26 n 29 SER 26 A THR 27 n 30 THR 27 A ASN 28 n 31 ASN 28 A TRP 29 n 32 TRP 29 A SER 30 n 33 SER 30 A ALA 31 n 34 ALA 31 A GLU 32 n 35 GLU 32 A ARG 33 n 36 ARG 33 A SER 34 n 37 SER 34 A ARG 35 n 38 ARG 35 A LEU 36 n 39 LEU 36 A ASN 37 n 40 ASN 37 A TYR 38 n 41 TYR 38 A PRO 39 n 42 PRO 39 A GLU 40 n 43 GLU 40 A ASN 41 n 44 ASN 41 A GLY 42 n 45 GLY 42 A TRP 43 n 46 TRP 43 A THR 44 n 47 THR 44 A PRO 45 n 48 PRO 45 A GLY 46 n 49 GLY 46 A GLU 47 n 50 GLU 47 A ASP 48 n 51 ASP 48 A SER 49 n 52 SER 49 A TYR 50 n 53 TYR 50 A ARG 51 n 54 ARG 51 A GLU 52 n 55 GLU 52 A TRP 53 n 56 TRP 53 A ILE 54 n 57 ILE 54 A GLN 55 n 58 GLN 55 A VAL 56 n 59 VAL 56 A ASP 57 n 60 ASP 57 A LEU 58 n 61 LEU 58 A GLY 59 n 62 GLY 59 A LEU 60 n 63 LEU 60 A LEU 61 n 64 LEU 61 A ARG 62 n 65 ARG 62 A PHE 63 n 66 PHE 63 A VAL 64 n 67 VAL 64 A THR 65 n 68 THR 65 A ALA 66 n 69 ALA 66 A VAL 67 n 70 VAL 67 A GLY 68 n 71 GLY 68 A THR 69 n 72 THR 69 A GLN 70 n 73 GLN 70 A GLY 71 n 74 GLY 71 A ALA 72 n 75 ALA 72 A ILE 73 n 76 ILE 73 A SER 74 n 77 SER 74 A LYS 75 n 78 LYS 75 A GLU 76 n 79 GLU 76 A THR 77 n 80 THR 77 A LYS 78 n 81 LYS 78 A LYS 79 n 82 LYS 79 A LYS 80 n 83 LYS 80 A TYR 81 n 84 TYR 81 A TYR 82 n 85 TYR 82 A VAL 83 n 86 VAL 83 A LYS 84 n 87 LYS 84 A THR 85 n 88 THR 85 A TYR 86 n 89 TYR 86 A LYS 87 n 90 LYS 87 A ILE 88 n 91 ILE 88 A ASP 89 n 92 ASP 89 A VAL 90 n 93 VAL 90 A SER 91 n 94 SER 91 A SER 92 n 95 SER 92 A ASN 93 n 96 ASN 93 A GLY 94 n 97 GLY 94 A GLU 95 n 98 GLU 95 A ASP 96 n 99 ASP 96 A TRP 97 n 100 TRP 97 A ILE 98 n 101 ILE 98 A THR 99 n 102 THR 99 A ILE 100 n 103 ILE 100 A LYS 101 n 104 LYS 101 A GLU 102 n 105 GLU 102 A GLY 103 n 106 GLY 103 A ASN 104 n 107 ASN 104 A LYS 105 n 108 LYS 105 A PRO 106 n 109 PRO 106 A VAL 107 n 110 VAL 107 A LEU 108 n 111 LEU 108 A PHE 109 n 112 PHE 109 A GLN 110 n 113 GLN 110 A GLY 111 n 114 GLY 111 A ASN 112 n 115 ASN 112 A THR 113 n 116 THR 113 A ASN 114 n 117 ASN 114 A PRO 115 n 118 PRO 115 A THR 116 n 119 THR 116 A ASP 117 n 120 ASP 117 A VAL 118 n 121 VAL 118 A VAL 119 n 122 VAL 119 A VAL 120 n 123 VAL 120 A ALA 121 n 124 ALA 121 A VAL 122 n 125 VAL 122 A PHE 123 n 126 PHE 123 A PRO 124 n 127 PRO 124 A LYS 125 n 128 LYS 125 A PRO 126 n 129 PRO 126 A LEU 127 n 130 LEU 127 A ILE 128 n 131 ILE 128 A THR 129 n 132 THR 129 A ARG 130 n 133 ARG 130 A PHE 131 n 134 PHE 131 A VAL 132 n 135 VAL 132 A ARG 133 n 136 ARG 133 A ILE 134 n 137 ILE 134 A LYS 135 n 138 LYS 135 A PRO 136 n 139 PRO 136 A ALA 137 n 140 ALA 137 A THR 138 n 141 THR 138 A TRP 139 n 142 TRP 139 A GLU 140 n 143 GLU 140 A THR 141 n 144 THR 141 A GLY 142 n 145 GLY 142 A ILE 143 n 146 ILE 143 A SER 144 n 147 SER 144 A MET 145 n 148 MET 145 A ARG 146 n 149 ARG 146 A PHE 147 n 150 PHE 147 A GLU 148 n 151 GLU 148 A VAL 149 n 152 VAL 149 A TYR 150 n 153 TYR 150 A GLY 151 n 154 GLY 151 A CYS 152 n 155 CYS 152 A LYS 153 n 156 LYS 153 A ILE 154 n 157 ILE 154 A THR 155 n 158 THR 155 A n 1 -2 B n 2 -1 B n 3 0 B n 4 1 B LYS 2 n 5 LYS 2 B CYS 3 n 6 CYS 3 B MET 4 n 7 MET 4 B GLU 5 n 8 GLU 5 B ALA 6 n 9 ALA 6 B LEU 7 n 10 LEU 7 B GLY 8 n 11 GLY 8 B MET 9 n 12 MET 9 B GLU 10 n 13 GLU 10 B SER 11 n 14 SER 11 B GLY 12 n 15 GLY 12 B GLU 13 n 16 GLU 13 B ILE 14 n 17 ILE 14 B HIS 15 n 18 HIS 15 B SER 16 n 19 SER 16 B ASP 17 n 20 ASP 17 B GLN 18 n 21 GLN 18 B ILE 19 n 22 ILE 19 B THR 20 n 23 THR 20 B ALA 21 n 24 ALA 21 B SER 22 n 25 SER 22 B SER 23 n 26 SER 23 B GLN 24 n 27 GLN 24 B TYR 25 n 28 TYR 25 B SER 26 n 29 SER 26 B THR 27 n 30 THR 27 B ASN 28 n 31 ASN 28 B TRP 29 n 32 TRP 29 B SER 30 n 33 SER 30 B ALA 31 n 34 ALA 31 B GLU 32 n 35 GLU 32 B ARG 33 n 36 ARG 33 B SER 34 n 37 SER 34 B ARG 35 n 38 ARG 35 B LEU 36 n 39 LEU 36 B ASN 37 n 40 ASN 37 B TYR 38 n 41 TYR 38 B PRO 39 n 42 PRO 39 B GLU 40 n 43 GLU 40 B ASN 41 n 44 ASN 41 B GLY 42 n 45 GLY 42 B TRP 43 n 46 TRP 43 B THR 44 n 47 THR 44 B PRO 45 n 48 PRO 45 B GLY 46 n 49 GLY 46 B GLU 47 n 50 GLU 47 B ASP 48 n 51 ASP 48 B SER 49 n 52 SER 49 B TYR 50 n 53 TYR 50 B ARG 51 n 54 ARG 51 B GLU 52 n 55 GLU 52 B TRP 53 n 56 TRP 53 B ILE 54 n 57 ILE 54 B GLN 55 n 58 GLN 55 B VAL 56 n 59 VAL 56 B ASP 57 n 60 ASP 57 B LEU 58 n 61 LEU 58 B GLY 59 n 62 GLY 59 B LEU 60 n 63 LEU 60 B LEU 61 n 64 LEU 61 B ARG 62 n 65 ARG 62 B PHE 63 n 66 PHE 63 B VAL 64 n 67 VAL 64 B THR 65 n 68 THR 65 B ALA 66 n 69 ALA 66 B VAL 67 n 70 VAL 67 B GLY 68 n 71 GLY 68 B THR 69 n 72 THR 69 B GLN 70 n 73 GLN 70 B GLY 71 n 74 GLY 71 B ALA 72 n 75 ALA 72 B ILE 73 n 76 ILE 73 B SER 74 n 77 SER 74 B LYS 75 n 78 LYS 75 B GLU 76 n 79 GLU 76 B THR 77 n 80 THR 77 B LYS 78 n 81 LYS 78 B LYS 79 n 82 LYS 79 B LYS 80 n 83 LYS 80 B TYR 81 n 84 TYR 81 B TYR 82 n 85 TYR 82 B VAL 83 n 86 VAL 83 B LYS 84 n 87 LYS 84 B THR 85 n 88 THR 85 B TYR 86 n 89 TYR 86 B LYS 87 n 90 LYS 87 B ILE 88 n 91 ILE 88 B ASP 89 n 92 ASP 89 B VAL 90 n 93 VAL 90 B SER 91 n 94 SER 91 B SER 92 n 95 SER 92 B ASN 93 n 96 ASN 93 B GLY 94 n 97 GLY 94 B GLU 95 n 98 GLU 95 B ASP 96 n 99 ASP 96 B TRP 97 n 100 TRP 97 B ILE 98 n 101 ILE 98 B THR 99 n 102 THR 99 B ILE 100 n 103 ILE 100 B LYS 101 n 104 LYS 101 B GLU 102 n 105 GLU 102 B GLY 103 n 106 GLY 103 B ASN 104 n 107 ASN 104 B LYS 105 n 108 LYS 105 B PRO 106 n 109 PRO 106 B VAL 107 n 110 VAL 107 B LEU 108 n 111 LEU 108 B PHE 109 n 112 PHE 109 B GLN 110 n 113 GLN 110 B GLY 111 n 114 GLY 111 B ASN 112 n 115 ASN 112 B THR 113 n 116 THR 113 B ASN 114 n 117 ASN 114 B PRO 115 n 118 PRO 115 B THR 116 n 119 THR 116 B ASP 117 n 120 ASP 117 B VAL 118 n 121 VAL 118 B VAL 119 n 122 VAL 119 B VAL 120 n 123 VAL 120 B ALA 121 n 124 ALA 121 B VAL 122 n 125 VAL 122 B PHE 123 n 126 PHE 123 B PRO 124 n 127 PRO 124 B LYS 125 n 128 LYS 125 B PRO 126 n 129 PRO 126 B LEU 127 n 130 LEU 127 B ILE 128 n 131 ILE 128 B THR 129 n 132 THR 129 B ARG 130 n 133 ARG 130 B PHE 131 n 134 PHE 131 B VAL 132 n 135 VAL 132 B ARG 133 n 136 ARG 133 B ILE 134 n 137 ILE 134 B LYS 135 n 138 LYS 135 B PRO 136 n 139 PRO 136 B ALA 137 n 140 ALA 137 B THR 138 n 141 THR 138 B TRP 139 n 142 TRP 139 B GLU 140 n 143 GLU 140 B THR 141 n 144 THR 141 B GLY 142 n 145 GLY 142 B ILE 143 n 146 ILE 143 B SER 144 n 147 SER 144 B MET 145 n 148 MET 145 B ARG 146 n 149 ARG 146 B PHE 147 n 150 PHE 147 B GLU 148 n 151 GLU 148 B VAL 149 n 152 VAL 149 B TYR 150 n 153 TYR 150 B GLY 151 n 154 GLY 151 B CYS 152 n 155 CYS 152 B LYS 153 n 156 LYS 153 B ILE 154 n 157 ILE 154 B THR 155 n 158 THR 155 B author_and_software_defined_assembly PISA 1 monomeric author_and_software_defined_assembly PISA 1 monomeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 A GLY -2 A GLY 1 1 Y 1 A HIS -1 A HIS 2 1 Y 1 A MET 0 A MET 3 1 Y 1 A PHE 1 A PHE 4 1 Y 1 B GLY -2 B GLY 1 1 Y 1 B HIS -1 B HIS 2 1 Y 1 B MET 0 B MET 3 1 Y 1 B PHE 1 B PHE 4 1 Y 1 9.31 1.50 119.30 128.61 A A A C N CA LYS PRO PRO 105 106 106 Y 1 A CYS 3 -151.50 77.95 1 A MET 4 -150.70 47.64 1 A SER 23 -170.08 -176.82 1 A SER 26 179.96 168.18 1 A TRP 29 -141.56 42.27 1 A ASN 41 59.59 -149.91 1 A ARG 51 -66.99 8.37 1 A LEU 60 179.69 167.05 1 A GLU 95 -120.23 -53.46 1 A PRO 106 -30.45 118.39 1 A ARG 130 -143.47 -36.17 1 A THR 141 71.05 -56.43 1 B SER 23 -171.15 -177.82 1 B SER 26 178.28 170.57 1 B TRP 29 -143.81 40.64 1 B ASN 41 58.13 -151.70 1 B LYS 78 76.88 -0.75 1 B ASN 93 -146.15 21.74 1 B ARG 130 -137.12 -38.57 1 B THR 141 72.22 -56.65 16.96 0.43000 0.00000 -0.14000 -0.82000 0.00000 0.35000 0.924 0.829 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.282 0.216 0.219 2.90 30.33 278 5573 4.800 87.8 30.153 0.280 RANDOM 1 THROUGHOUT MOLECULAR REPLACEMENT 0.585 0.80 0.80 1.20 PDB ENTRY 1KEX MAXIMUM LIKELIHOOD BABINET MODEL WITH MASK 2.90 30.33 8 2533 70 0 2455 0.012 0.022 2588 1.416 1.970 3513 4.432 5.000 306 30.513 24.182 110 14.543 15.000 438 17.784 15.000 14 0.082 0.200 376 0.003 0.020 1954 0.247 0.300 1156 0.332 0.500 1784 0.179 0.500 148 0.320 0.300 40 0.201 0.500 2 0.405 2.000 1569 0.660 3.000 2510 0.355 2.000 1195 0.561 3.000 1003 1 A 1 316 X-RAY DIFFRACTION tight positional 0.04 0.05 1 A 2 300 X-RAY DIFFRACTION tight positional 0.06 0.05 1 A 3 321 X-RAY DIFFRACTION tight positional 0.04 0.05 1 A 1 316 X-RAY DIFFRACTION tight thermal 0.07 0.50 1 A 2 300 X-RAY DIFFRACTION tight thermal 0.19 0.50 1 A 3 321 X-RAY DIFFRACTION tight thermal 0.16 0.50 0.341 0.297 2.97 15 396 20 83.20 2.900 30.33 3I97 5852 0.079 1 8.5000 2.400 88 0.191 2.9 3.0 4.0 2.3 85.4 data collection CrystalClear phasing PHASER refinement REFMAC 5.2.0019 data reduction d*TREK data scaling d*TREK B1 domain of human Neuropilin-1 bound with small molecule EG00229 1 N N 1 N N 2 N N 3 N N 2 N N 4 N N 4 N N A HIS 15 A HIS 18 HELX_P A ASP 17 A ASP 20 5 1 3 A SER 26 A SER 29 HELX_P A SER 34 A SER 37 5 2 9 B HIS 15 B HIS 18 HELX_P B ASP 17 B ASP 20 5 3 3 B SER 26 B SER 29 HELX_P B SER 34 B SER 37 5 4 9 disulf 2.019 A CYS 3 A SG CYS 6 1_555 A CYS 152 A SG CYS 155 1_555 disulf 2.043 B CYS 3 B SG CYS 6 1_555 B CYS 152 B SG CYS 155 1_555 SIGNALING PROTEIN Neuropilin-1, Drug, VEGF, Angiogenesis, Neuropilin, Alternative splicing, Cell membrane, Developmental protein, Differentiation, Disulfide bond, Glycoprotein, Heparan sulfate, Membrane, Neurogenesis, Phosphoprotein, Polymorphism, Proteoglycan, Receptor, Secreted, Transmembrane, MEMBRANE PROTEIN, SIGNALING PROTEIN A B A B A B A GLU 5 A GLU 8 A THR 44 A THR 47 1 B GLU 5 B GLU 8 B THR 44 B THR 47 1 A ILE 54 A ILE 57 A SER 91 A SER 94 1 B ILE 54 B ILE 57 B SER 91 B SER 94 1 A GLY 111 A GLY 114 A TYR 150 A TYR 153 1 B GLY 111 B GLY 114 B TYR 150 B TYR 153 1 NRP1_HUMAN UNP 1 273 O14786 FKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVDLGLLRFVTAVGTQGAISKETKKK YYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTDVVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKIT 273 427 3I97 1 155 O14786 A 1 4 158 273 427 3I97 1 155 O14786 B 1 4 158 1 expression tag GLY -2 3I97 A O14786 UNP 1 1 expression tag HIS -1 3I97 A O14786 UNP 2 1 expression tag MET 0 3I97 A O14786 UNP 3 2 expression tag GLY -2 3I97 B O14786 UNP 1 2 expression tag HIS -1 3I97 B O14786 UNP 2 2 expression tag MET 0 3I97 B O14786 UNP 3 BINDING SITE FOR RESIDUE 8DR A 156 A 8DR 156 Software 12 BINDING SITE FOR RESIDUE GOL A 157 A GOL 157 Software 3 BINDING SITE FOR RESIDUE 8DR B 156 B 8DR 156 Software 12 A TYR 25 A TYR 28 12 1_555 A SER 26 A SER 29 12 1_555 A THR 44 A THR 47 12 1_555 A ASP 48 A ASP 51 12 1_555 A SER 74 A SER 77 12 1_555 A GLU 76 A GLU 79 12 1_555 A THR 77 A THR 80 12 1_555 A TYR 81 A TYR 84 12 1_555 A GLY 142 A GLY 145 12 1_555 A ILE 143 A ILE 146 12 1_555 B MET 4 B MET 7 12 1_454 B VAL 120 B VAL 123 12 1_454 A SER 26 A SER 29 3 1_555 A THR 27 A THR 30 3 1_555 A ASN 28 A ASN 31 3 1_555 B TYR 25 B TYR 28 12 1_555 B SER 26 B SER 29 12 1_555 B ASN 28 B ASN 31 12 1_555 B TRP 29 B TRP 32 12 1_555 B THR 44 B THR 47 12 1_555 B ASP 48 B ASP 51 12 1_555 B SER 74 B SER 77 12 1_555 B GLU 76 B GLU 79 12 1_555 B THR 77 B THR 80 12 1_555 B TYR 81 B TYR 84 12 1_555 B GLY 142 B GLY 145 12 1_555 B ILE 143 B ILE 146 12 1_555 4 P 1 21 1