FAIRMol

Z45612920

Pose ID 12717 Compound 3713 Pose 516

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 Z45612920
PDB2WOV↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native mixed SASA done
Strain ΔE
14.0 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.26, Jaccard 0.17, H-bond role recall 0.00
Burial
92%
Hydrophobic fit
82%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.935 kcal/mol/HA) ✓ Good fit quality (FQ -8.83) ✓ Good H-bonds (3 bonds) ✓ Deep burial (92% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Moderate strain (14.0 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (3) ✗ Internal clashes (9)
Score
-26.181
kcal/mol
LE
-0.935
kcal/mol/HA
Fit Quality
-8.83
FQ (Leeson)
HAC
28
heavy atoms
MW
416
Da
LogP
5.35
cLogP
Strain ΔE
14.0 kcal/mol
SASA buried
92%
Lipo contact
82% BSA apolar/total
SASA unbound
656 Ų
Apolar buried
498 Ų

Interaction summary

HB 3 HY 21 PI 0 CLASH 2
Final rank0.424Score-26.181
Inter norm-1.117Intra norm0.137
Top1000noExcludedno
Contacts21H-bonds3
Artifact reasongeometry warning; 9 clashes; 3 protein contact clashes; 1 cofactor-context clash
Residues
ALA363 ALA365 ARG287 CYS57 GLN439 GLY56 ILE199 ILE438 LEU334 LYS60 NDP800 PHE182 PHE203 PHE367 PRO336 PRO435 SER178 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 overlap7Native recall0.26
Jaccard0.17RMSD-
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
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
516 0.4241926104561533 -1.1173 -26.1813 3 21 7 0.26 0.00 - no Current
541 2.5898260359995993 -0.875689 -22.4799 3 15 0 0.00 0.00 - no Open
533 4.94459793995519 -1.07721 -29.0291 7 18 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 -26.181kcal/mol
Ligand efficiency (LE) -0.9350kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.827
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 416.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.35
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 14.02kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 6.95kcal/mol
Minimised FF energy -7.08kcal/mol

SASA & burial

✓ computed
SASA (unbound) 655.7Ų
Total solvent-accessible surface area of free ligand
BSA total 604.9Ų
Buried surface area upon binding
BSA apolar 498.3Ų
Hydrophobic contacts buried
BSA polar 106.5Ų
Polar contacts buried
Fraction buried 92.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3124.8Ų
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 1479.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)