FAIRMol

Z56071437

Pose ID 14838 Compound 311 Pose 600

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
T22
L. donovani rab5a L. donovani
Ligand Z56071437

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 strong SASA done
Strain ΔE
32.0 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.76, Jaccard 0.67, H-bond role recall 0.45
Burial
80%
Hydrophobic fit
79%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular 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 (-1.072 kcal/mol/HA) ✓ Good fit quality (FQ -10.44) ✓ Strong H-bond network (13 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Very high strain energy (32.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-33.224
kcal/mol
LE
-1.072
kcal/mol/HA
Fit Quality
-10.44
FQ (Leeson)
HAC
31
heavy atoms
MW
500
Da
LogP
5.50
cLogP
Strain ΔE
32.0 kcal/mol
SASA buried
80%
Lipo contact
79% BSA apolar/total
SASA unbound
747 Ų
Apolar buried
468 Ų

Interaction summary

HB 13 HY 2 PI 0 CLASH 3 ⚠ 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 5.5 H-bonds 13
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
Final rank3.987Score-33.224
Inter norm-1.084Intra norm0.012
Top1000noExcludedno
Contacts19H-bonds13
Artifact reasongeometry warning; 13 clashes; 2 protein clashes; high strain Δ 32.0
Residues
ALA24 ASP129 GLN42 GLU21 GLU73 GLY23 GLY25 GLY71 LEU130 LEU39 LYS127 LYS159 LYS26 PHE38 SER22 SER27 SER28 THR44 THR69

Protein summary

165 residues
Protein targetT22Atoms2561
Residues165Chains1
Residue summaryLEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameRAB5AContacts21
PoseOpen native poseHB0
IFP residues
ALA158 ALA24 ALA40 ASN126 ASN41 ASP129 GLN42 GLU21 GLU73 GLY23 GLY25 LEU130 LEU39 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28
Current overlap16Native recall0.76
Jaccard0.67RMSD-
HB strict6Strict recall0.40
HB same residue+role5HB role recall0.45
HB same residue6HB residue recall0.55

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
572 0.5870117947832066 -1.10765 -37.5989 7 16 0 0.00 0.00 - no Open
583 0.8823549273857154 -0.910836 -30.2227 2 20 0 0.00 0.00 - no Open
592 1.310495564240597 -0.754262 -27.3292 4 16 0 0.00 0.00 - no Open
611 1.7798849023795245 -0.802683 -26.2147 4 16 0 0.00 0.00 - no Open
594 1.9412230667148331 -0.877204 -32.0703 1 19 0 0.00 0.00 - no Open
584 2.0822003114507757 -0.856641 -25.7246 2 18 0 0.00 0.00 - no Open
583 2.606119674997513 -0.894636 -26.6402 9 16 0 0.00 0.00 - no Open
600 2.62217074979796 -0.689693 -24.6956 3 8 0 0.00 0.00 - no Open
575 3.3580502961066707 -0.8137 -25.6478 3 15 0 0.00 0.00 - no Open
595 3.5009994029016003 -0.774293 -24.4273 4 21 1 0.05 0.00 - no Open
587 3.744243536944524 -0.642671 -23.6962 5 10 0 0.00 0.00 - no Open
600 3.987159201366124 -1.08362 -33.2245 13 19 16 0.76 0.45 - no Current
591 6.027892840267617 -0.912188 -27.1412 8 19 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 -33.224kcal/mol
Ligand efficiency (LE) -1.0718kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.441
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 500.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.50
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 32.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -25.16kcal/mol
Minimised FF energy -57.20kcal/mol

SASA & burial

✓ computed
SASA (unbound) 747.4Ų
Total solvent-accessible surface area of free ligand
BSA total 594.3Ų
Buried surface area upon binding
BSA apolar 468.3Ų
Hydrophobic contacts buried
BSA polar 126.0Ų
Polar contacts buried
Fraction buried 79.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1438.6Ų
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 1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 526.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)