FAIRMol

Z19459210

Pose ID 9188 Compound 944 Pose 380

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
T14
T. brucei ODC (G418 binding site) T. brucei G418 binding site
Ligand Z19459210
PDB1NJJ↗

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 high Native mixed SASA done
Strain ΔE
25.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.53, Jaccard 0.38, H-bond role recall 0.40
Burial
70%
Hydrophobic fit
68%
Reason: no major geometry red flags detected
1 protein-contact clashes 71% of hydrophobic surface is solvent-exposed (15/21 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 (-0.610 kcal/mol/HA) ✓ Good fit quality (FQ -6.00) ✓ Strong H-bond network (13 bonds) ✓ Deep burial (70% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ High strain energy (25.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-19.510
kcal/mol
LE
-0.610
kcal/mol/HA
Fit Quality
-6.00
FQ (Leeson)
HAC
32
heavy atoms
MW
458
Da
LogP
3.57
cLogP
Strain ΔE
25.4 kcal/mol
SASA buried
70%
Lipo contact
68% BSA apolar/total
SASA unbound
725 Ų
Apolar buried
347 Ų

Interaction summary

HB 13 HY 1 PI 0 CLASH 1 ⚠ Exposure 71%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
71% of hydrophobic surface is solvent-exposed (15/21 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 21 Buried (contacted) 6 Exposed 15 LogP 3.57 H-bonds 13
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (2/5 atoms exposed)phenyl (3/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
Final rank2.390Score-19.510
Inter norm-0.734Intra norm0.124
Top1000noExcludedno
Contacts14H-bonds13
Artifact reasongeometry warning; 10 clashes; 1 protein clash; moderate strain Δ 25.4
Residues
ARG242 ARG337 ARG50 ASP243 ASP385 ASP47 GLU384 GLY240 LEU339 LYS51 PHE383 SER282 THR241 TYR370

Protein summary

398 residues
Protein targetT14Atoms6140
Residues398Chains1
Residue summaryVAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170

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:ORX602

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1NJJContacts15
PoseOpen native poseHB0
IFP residues
ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241
Current overlap8Native recall0.53
Jaccard0.38RMSD-
HB strict1Strict recall0.17
HB same residue+role2HB role recall0.40
HB same residue3HB residue recall0.60

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
353 0.2677846330097941 -1.07537 -27.8222 8 17 0 0.00 0.00 - no Open
385 1.072504017808142 -0.997956 -27.1257 7 18 0 0.00 0.00 - no Open
335 1.9579738510770275 -1.01092 -28.7026 6 22 0 0.00 0.00 - no Open
382 2.0108526982107993 -0.822339 -20.3127 6 13 0 0.00 0.00 - no Open
380 2.3895493898087743 -0.733724 -19.5103 13 14 8 0.53 0.40 - no Current
451 2.500575774493837 -0.801352 -19.5984 4 18 0 0.00 0.00 - no Open
365 2.585210403258686 -0.744596 -11.1465 9 20 0 0.00 0.00 - no Open
397 3.1112027661132537 -0.667648 -14.8384 8 10 0 0.00 0.00 - no Open
398 3.193158610637237 -0.881209 -19.5521 15 18 0 0.00 0.00 - no Open
436 3.954326897652338 -0.726205 -12.1702 7 19 0 0.00 0.00 - no Open
337 4.153204340630617 -0.904158 -19.2488 9 13 0 0.00 0.00 - no Open
346 5.166667667365341 -0.742034 -19.6346 11 13 0 0.00 0.00 - no Open
361 5.606440624303128 -1.02946 -25.164 13 16 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 -19.510kcal/mol
Ligand efficiency (LE) -0.6097kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.996
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 458.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.57
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 25.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 100.87kcal/mol
Minimised FF energy 75.46kcal/mol

SASA & burial

✓ computed
SASA (unbound) 725.4Ų
Total solvent-accessible surface area of free ligand
BSA total 510.9Ų
Buried surface area upon binding
BSA apolar 347.2Ų
Hydrophobic contacts buried
BSA polar 163.7Ų
Polar contacts buried
Fraction buried 70.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2445.1Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1382.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)