FAIRMol

NMT-TY0959

Pose ID 2383 Compound 527 Pose 350

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T04
L. major PTR1 L. major
Ligand NMT-TY0959
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
32.9 kcal/mol
Protein clashes
0
Internal clashes
9
Native overlap
contact recall 0.63, Jaccard 0.60, H-bond role recall 0.00
Burial
77%
Hydrophobic fit
71%
Reason: 9 internal clashes
9 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.922 kcal/mol/HA) ✓ Good fit quality (FQ -8.60) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ Very high strain energy (32.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-24.885
kcal/mol
LE
-0.922
kcal/mol/HA
Fit Quality
-8.60
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.27
cLogP
Strain ΔE
32.9 kcal/mol
SASA buried
77%
Lipo contact
71% BSA apolar/total
SASA unbound
636 Ų
Apolar buried
349 Ų

Interaction summary

HB 2 HY 18 PI 3 CLASH 0
Final rank0.363Score-24.885
Inter norm-0.926Intra norm0.005
Top1000noExcludedno
Contacts13H-bonds2
Artifact reasongeometry warning; 9 clashes; 1 protein contact clash; high strain Δ 32.9
Residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 MET233 NDP302 PHE113 TYR191 TYR194 VAL237 ARG287

Protein summary

308 residues
Protein targetT04Atoms4210
Residues308Chains3
Residue summaryLEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:NDP302

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name7PXXContacts19
PoseOpen native poseHB0
IFP residues
ARG17 ASP181 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER112 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap12Native recall0.63
Jaccard0.60RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
350 0.3629211958252925 -0.926251 -24.8853 2 13 12 0.63 0.00 - no Current
308 0.8712687604222177 -1.14475 -30.9484 7 15 0 0.00 0.00 - no Open
313 1.3142726160638258 -1.30957 -33.6603 12 15 0 0.00 0.00 - no Open
337 1.7652358533706136 -0.983958 -24.6706 6 21 0 0.00 0.00 - no Open
326 1.9773175739360493 -1.1336 -31.1195 10 21 0 0.00 0.00 - no Open
291 2.165473959343045 -1.26034 -34.3636 9 22 0 0.00 0.00 - no Open
301 2.480529293523874 -1.03512 -28.7525 9 12 12 0.63 0.60 - no Open
391 2.9008417563283935 -1.06217 -28.0759 7 15 0 0.00 0.00 - no Open
405 2.9806369013586718 -1.18262 -29.8648 6 15 0 0.00 0.00 - no Open
381 3.0321874169205607 -1.08611 -28.6887 6 16 0 0.00 0.00 - no Open
379 3.2808649478445537 -0.969429 -25.6956 10 17 0 0.00 0.00 - no Open
332 3.3588118370115048 -1.08116 -27.9486 7 17 0 0.00 0.00 - no Open
416 3.387046221950613 -0.924839 -25.7132 8 13 0 0.00 0.00 - no Open
334 3.429500560915679 -1.04914 -24.4852 8 15 0 0.00 0.00 - no Open
349 3.654496302035269 -0.850128 -21.98 8 14 0 0.00 0.00 - no Open
302 3.8731875216797746 -1.1408 -30.4082 8 22 0 0.00 0.00 - no Open
286 4.0813402406540185 -0.908062 -25.3939 13 15 0 0.00 0.00 - no Open
358 4.09740218547716 -0.710564 -18.8071 6 10 0 0.00 0.00 - no Open
336 4.132326379777683 -0.942975 -24.3804 7 17 0 0.00 0.00 - no Open
453 4.769829786717276 -1.02855 -27.026 8 17 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -24.885kcal/mol
Ligand efficiency (LE) -0.9217kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.599
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.27
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 32.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -62.02kcal/mol
Minimised FF energy -94.88kcal/mol

SASA & burial

✓ computed
SASA (unbound) 635.7Ų
Total solvent-accessible surface area of free ligand
BSA total 489.3Ų
Buried surface area upon binding
BSA apolar 348.6Ų
Hydrophobic contacts buried
BSA polar 140.6Ų
Polar contacts buried
Fraction buried 77.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1626.6Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1024.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)