FAIRMol

Z49891479

Pose ID 12616 Compound 818 Pose 415

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 Z49891479
PDB2WOV↗

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 mixed SASA done
Strain ΔE
25.0 kcal/mol
Protein clashes
0
Internal clashes
7
Native overlap
contact recall 0.30, Jaccard 0.24, H-bond role recall 0.00
Burial
91%
Hydrophobic fit
71%
Reason: 7 internal clashes
7 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.297 kcal/mol/HA) ✓ Good fit quality (FQ -11.63) ✓ Good H-bonds (5 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ High strain energy (25.0 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-31.135
kcal/mol
LE
-1.297
kcal/mol/HA
Fit Quality
-11.63
FQ (Leeson)
HAC
24
heavy atoms
MW
340
Da
LogP
3.34
cLogP
Strain ΔE
25.0 kcal/mol
SASA buried
91%
Lipo contact
71% BSA apolar/total
SASA unbound
561 Ų
Apolar buried
363 Ų

Interaction summary

HB 5 HY 17 PI 0 CLASH 0
Final rank2.265Score-31.135
Inter norm-1.317Intra norm0.020
Top1000noExcludedno
Contacts15H-bonds5
Artifact reasongeometry warning; 7 clashes; 2 protein clashes; moderate strain Δ 25.0
Residues
ALA365 ARG287 ASP327 CYS57 GLY56 ILE199 LEU334 LYS60 MET333 NDP800 PHE367 PRO336 SER364 THR335 THR51

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
Jaccard0.24RMSD-
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
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
459 0.9834178066983842 -1.01619 -22.8206 8 15 0 0.00 0.00 - no Open
489 1.3935518030020047 -0.99865 -20.7043 3 12 0 0.00 0.00 - no Open
494 1.654975662962992 -1.07605 -28.4398 4 15 0 0.00 0.00 - no Open
450 1.8221991932961779 -0.948948 -19.4208 7 12 0 0.00 0.00 - no Open
432 2.0626620653116463 -1.06385 -22.0827 10 14 0 0.00 0.00 - no Open
415 2.2651134184818567 -1.3172 -31.1352 5 15 8 0.30 0.00 - no Current
515 2.8696934123764937 -0.963412 -19.4317 4 10 0 0.00 0.00 - no Open
406 3.633375166152976 -1.19736 -29.6559 6 14 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 -31.135kcal/mol
Ligand efficiency (LE) -1.2973kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.626
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 340.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.34
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 25.02kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 83.64kcal/mol
Minimised FF energy 58.62kcal/mol

SASA & burial

✓ computed
SASA (unbound) 561.2Ų
Total solvent-accessible surface area of free ligand
BSA total 510.8Ų
Buried surface area upon binding
BSA apolar 363.2Ų
Hydrophobic contacts buried
BSA polar 147.5Ų
Polar contacts buried
Fraction buried 91.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3001.9Ų
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 1473.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)