FAIRMol

ulfkktlib_2577

Pose ID 9021 Compound 3192 Pose 213

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 ulfkktlib_2577
PDB1NJJ↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
41.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.53, Jaccard 0.33, H-bond role recall 0.20
Burial
79%
Hydrophobic fit
93%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 73% of hydrophobic surface is solvent-exposed (19/26 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 ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.650 kcal/mol/HA) ✓ Good fit quality (FQ -6.45) ✓ Good H-bonds (4 bonds) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (93%) ✗ Extreme strain energy (41.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-21.461
kcal/mol
LE
-0.650
kcal/mol/HA
Fit Quality
-6.45
FQ (Leeson)
HAC
33
heavy atoms
MW
445
Da
LogP
1.56
cLogP
Strain ΔE
41.1 kcal/mol
SASA buried
79%
Lipo contact
93% BSA apolar/total
SASA unbound
782 Ų
Apolar buried
579 Ų

Interaction summary

HB 4 HY 4 PI 0 CLASH 3 ⚠ Exposure 73%

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
73% of hydrophobic surface is solvent-exposed (19/26 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 26 Buried (contacted) 7 Exposed 19 LogP 1.56 H-bonds 4
Exposed fragments: phenyl (5/6 atoms exposed)phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (7 atoms exposed)
Final rank3.726Score-21.461
Inter norm-0.756Intra norm0.106
Top1000noExcludedno
Contacts17H-bonds4
Artifact reasongeometry warning; 13 clashes; 2 protein clashes; high strain Δ 41.1
Residues
ALA283 ARG242 ARG337 ASP243 ASP385 ASP44 ASP47 GLU384 GLY240 LEU339 LYS51 PHE284 PHE383 SER282 THR21 THR241 THR285

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
Jaccard0.33RMSD-
HB strict0Strict recall0.00
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
170 1.039511345490578 -0.770394 -25.9281 2 19 0 0.00 0.00 - no Open
213 3.726325550996569 -0.756128 -21.4612 4 17 8 0.53 0.20 - no Current
168 4.0277132181428845 -0.938673 -29.2755 6 25 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 -21.461kcal/mol
Ligand efficiency (LE) -0.6503kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.453
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 444.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.56
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 41.08kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 59.90kcal/mol
Minimised FF energy 18.82kcal/mol

SASA & burial

✓ computed
SASA (unbound) 781.6Ų
Total solvent-accessible surface area of free ligand
BSA total 620.8Ų
Buried surface area upon binding
BSA apolar 579.0Ų
Hydrophobic contacts buried
BSA polar 41.8Ų
Polar contacts buried
Fraction buried 79.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 93.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2676.4Ų
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 1379.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)