FAIRMol

Z92413403

Pose ID 12838 Compound 65 Pose 637

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 Z92413403
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
Weak or marginal quality
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
37.3 kcal/mol
Protein clashes
3
Internal clashes
5
Native overlap
contact recall 0.44, Jaccard 0.39, H-bond role recall 0.20
Burial
82%
Hydrophobic fit
62%
Reason: no major geometry red flags detected
3 protein-contact clashes 5 intramolecular clashes 67% of hydrophobic surface is solvent-exposed (12/18 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.933 kcal/mol/HA) ✓ Good fit quality (FQ -8.91) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (62%) ✗ Very high strain energy (37.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-27.062
kcal/mol
LE
-0.933
kcal/mol/HA
Fit Quality
-8.91
FQ (Leeson)
HAC
29
heavy atoms
MW
431
Da
LogP
2.05
cLogP
Strain ΔE
37.3 kcal/mol
SASA buried
82%
Lipo contact
62% BSA apolar/total
SASA unbound
667 Ų
Apolar buried
343 Ų

Interaction summary

HB 8 HY 7 PI 0 CLASH 5 ⚠ Exposure 66%

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
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
67% of hydrophobic surface is solvent-exposed (12/18 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 18 Buried (contacted) 6 Exposed 12 LogP 2.05 H-bonds 8
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (2/5 atoms exposed)phenyl (3/3 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank1.586Score-27.062
Inter norm-1.227Intra norm0.294
Top1000noExcludedno
Contacts16H-bonds8
Artifact reasongeometry warning; 7 clashes; 1 protein clash; 2 severe cofactor-context clashes; high strain Δ 37.3
Residues
ARG222 ARG228 ARG287 ASP330 GLN165 GLY196 GLY197 GLY286 ILE285 LEU227 LEU332 LYS306 MET333 NDP800 PHE198 PHE230

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 overlap12Native recall0.44
Jaccard0.39RMSD-
HB strict1Strict recall0.08
HB same residue+role1HB role recall0.20
HB same residue2HB residue recall0.50

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
621 0.7553128777043048 -0.907356 -22.9807 5 17 0 0.00 0.00 - no Open
614 0.8508650150709747 -1.12527 -31.6 5 21 0 0.00 0.00 - no Open
637 1.5864418633829753 -1.22686 -27.0617 8 16 12 0.44 0.20 - no Current
622 1.9656959157672311 -0.995348 -24.1395 7 14 0 0.00 0.00 - no Open
641 2.1976977249631062 -0.929194 -24.5255 5 20 0 0.00 0.00 - no Open
627 2.3110603471039823 -0.976209 -19.9778 16 17 0 0.00 0.00 - no Open
635 3.7507071858182983 -0.724276 -17.5318 6 11 0 0.00 0.00 - no Open
630 4.416198630356118 -1.08354 -25.6992 6 13 0 0.00 0.00 - no Open
631 5.242837036640544 -0.891898 -20.2023 13 17 0 0.00 0.00 - no Open
650 5.49701072979079 -1.06926 -25.805 12 23 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 -27.062kcal/mol
Ligand efficiency (LE) -0.9332kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.908
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 430.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.05
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 37.29kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -35.94kcal/mol
Minimised FF energy -73.23kcal/mol

SASA & burial

✓ computed
SASA (unbound) 666.7Ų
Total solvent-accessible surface area of free ligand
BSA total 549.7Ų
Buried surface area upon binding
BSA apolar 343.2Ų
Hydrophobic contacts buried
BSA polar 206.5Ų
Polar contacts buried
Fraction buried 82.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 62.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2971.9Ų
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 1527.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)