Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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
35.8 kcal/mol
Protein clashes
10
Internal clashes
10
Native overlap
contact recall 0.52, Jaccard 0.35, H-bond role recall 0.45
Reason: 10 protein-contact clashes, 10 internal clashes
10 protein-contact clashes
10 intramolecular clashes
77% of hydrophobic surface is solvent-exposed (10/13 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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.299 kcal/mol/HA)
✓ Good fit quality (FQ -11.47)
✓ Strong H-bond network (16 bonds)
✓ Deep burial (94% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ Very high strain energy (35.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-29.885
kcal/mol
LE
-1.299
kcal/mol/HA
Fit Quality
-11.47
FQ (Leeson)
HAC
23
heavy atoms
MW
353
Da
LogP
1.01
cLogP
Interaction summary
HB 16
HY 4
PI 0
CLASH 10
⚠ Exposure 76%
Interaction summary
HB 16
HY 4
PI 0
CLASH 10
⚠ Exposure 76%
Solvent-exposed hydrophobic surface — desolvation penalty likely
77% of hydrophobic surface is solvent-exposed (10/13 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 13
Buried (contacted) 3
Exposed 10
LogP 1.01
H-bonds 16
Exposed fragments:
phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)
| Final rank | 5.371 | Score | -29.885 |
|---|---|---|---|
| Inter norm | -1.314 | Intra norm | 0.014 |
| Top1000 | no | Excluded | no |
| Contacts | 21 | H-bonds | 16 |
| Artifact reason | geometry warning; 9 clashes; 3 protein clashes; high strain Δ 35.7 | ||
| Residues |
ALA24
ALA70
ASP68
GLN42
GLU21
GLU43
GLU73
GLY23
GLY25
GLY47
GLY71
ILE46
LEU31
LEU39
LYS26
SER22
SER27
SER28
THR44
THR45
THR69
| ||
Protein summary
165 residues
| Protein target | T22 | Atoms | 2561 |
|---|---|---|---|
| Residues | 165 | Chains | 1 |
| Residue summary | LEU: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.
| Name | RAB5A | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU21
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
| ||
| Current overlap | 11 | Native recall | 0.52 |
| Jaccard | 0.35 | RMSD | - |
| HB strict | 6 | Strict recall | 0.40 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 5 | HB residue recall | 0.45 |
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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 316 | 1.9160126527138646 | -0.936024 | -21.449 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 278 | 1.9632061033636858 | -1.23187 | -29.5802 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 335 | 2.279560783148469 | -0.836864 | -20.633 | 9 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 298 | 2.4959341423803725 | -1.18433 | -27.7045 | 6 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 350 | 2.8871935436214495 | -1.13026 | -23.8892 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 328 | 3.34922510797409 | -0.990588 | -23.4443 | 11 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 385 | 3.5748823696267844 | -1.1536 | -27.6164 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 347 | 3.741128851709964 | -1.38593 | -32.0766 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 366 | 3.895818972211368 | -1.29627 | -28.5384 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 339 | 4.420406439957224 | -0.972962 | -25.0114 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 248 | 4.628592872571314 | -1.0994 | -24.8798 | 15 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 288 | 5.3707651519523365 | -1.31364 | -29.8849 | 16 | 21 | 11 | 0.52 | 0.45 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.885kcal/mol
Ligand efficiency (LE)
-1.2993kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.468
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
353.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.01
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.80kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-83.01kcal/mol
Minimised FF energy
-118.81kcal/mol
SASA & burial
✓ computed
SASA (unbound)
562.3Ų
Total solvent-accessible surface area of free ligand
BSA total
530.4Ų
Buried surface area upon binding
BSA apolar
352.6Ų
Hydrophobic contacts buried
BSA polar
177.8Ų
Polar contacts buried
Fraction buried
94.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1245.3Ų
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
500.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)