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 high
Native strong
SASA done
Strain ΔE
25.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.76, Jaccard 0.59, H-bond role recall 0.36
Reason: no major geometry red flags detected
2 protein-contact clashes
43% of hydrophobic surface appears solvent-exposed (9/21 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 (-1.307 kcal/mol/HA)
✓ Good fit quality (FQ -12.04)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (93% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ High strain energy (25.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-33.976
kcal/mol
LE
-1.307
kcal/mol/HA
Fit Quality
-12.04
FQ (Leeson)
HAC
26
heavy atoms
MW
344
Da
LogP
3.80
cLogP
Interaction summary
HB 10
HY 6
PI 1
CLASH 2
⚠ Exposure 42%
Interaction summary
HB 10
HY 6
PI 1
CLASH 2
⚠ Exposure 42%
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
Partial hydrophobic solvent exposure
43% of hydrophobic surface appears solvent-exposed (9/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 21
Buried (contacted) 12
Exposed 9
LogP 3.8
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 5.131 | Score | -33.976 |
|---|---|---|---|
| Inter norm | -1.348 | Intra norm | 0.041 |
| Top1000 | no | Excluded | no |
| Contacts | 22 | H-bonds | 10 |
| Artifact reason | geometry warning; 14 clashes; 3 protein clashes; moderate strain Δ 25.9 | ||
| Residues |
ALA24
ALA40
ASN126
ASN41
GLN42
GLU21
GLU43
GLU73
GLY23
GLY25
GLY47
GLY71
LEU31
LEU39
LYS127
LYS26
PHE38
SER22
SER27
SER28
THR44
THR69
| ||
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 | 16 | Native recall | 0.76 |
| Jaccard | 0.59 | 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 |
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 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 534 | 1.2420259156033218 | -1.37104 | -39.8358 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 541 | 1.4772504244595919 | -1.33625 | -37.8164 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 565 | 2.479557913822649 | -0.983468 | -27.7945 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 591 | 3.304379984241723 | -0.903165 | -22.4239 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 557 | 5.130585228551614 | -1.3476 | -33.9762 | 10 | 22 | 16 | 0.76 | 0.36 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-33.976kcal/mol
Ligand efficiency (LE)
-1.3068kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.040
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
344.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.80
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.88kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
121.39kcal/mol
Minimised FF energy
95.51kcal/mol
SASA & burial
✓ computed
SASA (unbound)
559.8Ų
Total solvent-accessible surface area of free ligand
BSA total
519.8Ų
Buried surface area upon binding
BSA apolar
401.5Ų
Hydrophobic contacts buried
BSA polar
118.3Ų
Polar contacts buried
Fraction buried
92.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1299.8Ų
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
504.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)