FAIRMol

Z49582855

Pose ID 12601 Compound 1194 Pose 400

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
T19
T. brucei TR (NADPH binding site) T. brucei NADPH binding site
Ligand Z49582855
PDB2WOV↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
65.2 kcal/mol
Protein clashes
3
Internal clashes
4
Native overlap
contact recall 0.30, Jaccard 0.21, H-bond role recall 0.60
Burial
94%
Hydrophobic fit
80%
Reason: strain 65.2 kcal/mol
strain ΔE 65.2 kcal/mol 3 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.894 kcal/mol/HA) ✓ Good fit quality (FQ -8.87) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Extreme strain energy (65.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-29.488
kcal/mol
LE
-0.894
kcal/mol/HA
Fit Quality
-8.87
FQ (Leeson)
HAC
33
heavy atoms
MW
466
Da
LogP
4.22
cLogP
Strain ΔE
65.2 kcal/mol
SASA buried
94%
Lipo contact
80% BSA apolar/total
SASA unbound
690 Ų
Apolar buried
518 Ų

Interaction summary

HB 8 HY 16 PI 1 CLASH 4
Final rank2.920Score-29.488
Inter norm-0.993Intra norm0.099
Top1000noExcludedno
Contacts20H-bonds8
Artifact reasongeometry warning; 16 clashes; 1 protein clash; 1 cofactor-context clash; high strain Δ 61.1
Residues
ALA363 ALA365 ARG287 ASP327 CYS52 CYS57 GLY56 ILE199 LEU334 LYS60 MET333 NDP800 PHE367 PRO336 SER14 SER162 SER364 THR335 THR51 VAL55

Protein summary

493 residues
Protein targetT19Atoms7541
Residues493Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:330; TYR:294; ASP:264; MET:221

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
C:NDP800

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name2WOVContacts27
PoseOpen native poseHB0
IFP residues
ALA284 ALA365 ARG222 ARG228 ARG287 ASN223 ASN254 GLN165 GLU202 GLY195 GLY196 GLY197 GLY286 ILE199 ILE285 LEU227 LEU334 LYS60 MET333 NDP800 PHE198 PHE367 PRO167 SER200 TYR221 VAL194 VAL366
Current overlap8Native recall0.30
Jaccard0.21RMSD-
HB strict3Strict recall0.25
HB same residue+role3HB role recall0.60
HB same residue2HB residue recall0.50

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
459 1.829936886186891 -0.833233 -18.1042 4 9 0 0.00 0.00 - no Open
400 2.919528348790917 -0.992687 -29.4876 8 20 8 0.30 0.60 - no Current
443 5.2170465664104695 -0.651954 -13.936 6 9 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 -29.488kcal/mol
Ligand efficiency (LE) -0.8936kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.866
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 466.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.22
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 65.20kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 120.02kcal/mol
Minimised FF energy 54.81kcal/mol

SASA & burial

✓ computed
SASA (unbound) 689.8Ų
Total solvent-accessible surface area of free ligand
BSA total 646.9Ų
Buried surface area upon binding
BSA apolar 517.6Ų
Hydrophobic contacts buried
BSA polar 129.3Ų
Polar contacts buried
Fraction buried 93.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3137.9Ų
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 4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1487.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)