Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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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
30.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.86, Jaccard 0.72, H-bond role recall 0.36
Reason: no major geometry red flags detected
1 protein-contact clashes
38% of hydrophobic surface appears solvent-exposed (6/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.300 kcal/mol/HA)
✓ Good fit quality (FQ -11.97)
✓ Strong H-bond network (14 bonds)
✓ Deep burial (91% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Very high strain energy (30.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-33.788
kcal/mol
LE
-1.300
kcal/mol/HA
Fit Quality
-11.97
FQ (Leeson)
HAC
26
heavy atoms
MW
396
Da
LogP
2.16
cLogP
Interaction summary
HB 14
HY 6
PI 1
CLASH 1
⚠ Exposure 37%
Interaction summary
HB 14
HY 6
PI 1
CLASH 1
⚠ Exposure 37%
Partial hydrophobic solvent exposure
38% of hydrophobic surface appears solvent-exposed (6/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 16
Buried (contacted) 10
Exposed 6
LogP 2.16
H-bonds 14
Exposed fragments:
phenyl (6/6 atoms exposed)
| Final rank | 2.385 | Score | -33.788 |
|---|---|---|---|
| Inter norm | -1.304 | Intra norm | 0.004 |
| Top1000 | no | Excluded | no |
| Contacts | 22 | H-bonds | 14 |
| Artifact reason | geometry warning; 12 clashes; 1 protein clash; high strain Δ 30.5 | ||
| Residues |
ALA24
ALA40
ALA70
ASN126
ASN41
ASP129
GLN42
GLU73
GLY23
GLY25
GLY71
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER27
SER28
THR44
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 | 18 | Native recall | 0.86 |
| Jaccard | 0.72 | RMSD | - |
| HB strict | 5 | Strict recall | 0.33 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 323 | 0.604003958058523 | -0.942657 | -21.1902 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 291 | 0.6323186320960439 | -1.22038 | -30.9952 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 329 | 1.875810958250805 | -0.873591 | -23.2439 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 290 | 2.002828557753335 | -1.14993 | -29.8501 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 310 | 2.224044674964138 | -0.998085 | -25.5439 | 8 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 274 | 2.2594370727836455 | -1.19735 | -30.4625 | 8 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 363 | 2.3368706908166565 | -1.24065 | -32.9492 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 296 | 2.3850699368176747 | -1.30385 | -33.7876 | 14 | 22 | 18 | 0.86 | 0.36 | - | no | Current |
| 256 | 2.4947555472898184 | -0.974719 | -18.8557 | 12 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 354 | 2.712760058770864 | -1.25519 | -32.5296 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 425 | 3.1536405973770054 | -1.02037 | -26.076 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 270 | 3.5240590701875685 | -1.13687 | -30.0974 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 349 | 3.8084335922387926 | -0.992658 | -26.3696 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 380 | 3.892965236960112 | -1.26373 | -32.5926 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 394 | 4.604769733373062 | -0.872118 | -21.6077 | 9 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-33.788kcal/mol
Ligand efficiency (LE)
-1.2995kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.973
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
395.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.16
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-18.55kcal/mol
Minimised FF energy
-49.03kcal/mol
SASA & burial
✓ computed
SASA (unbound)
633.3Ų
Total solvent-accessible surface area of free ligand
BSA total
575.3Ų
Buried surface area upon binding
BSA apolar
432.2Ų
Hydrophobic contacts buried
BSA polar
143.1Ų
Polar contacts buried
Fraction buried
90.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1341.2Ų
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
494.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)